| Contributors |
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| Preface |
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xvii | |
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1 Fundamentals of neutron crystallography in structural biology |
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1 | (20) |
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2 | (2) |
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2 Basics of neutrons as a diffraction probe |
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4 | (5) |
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3 Types of neutron sources |
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9 | (1) |
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4 Neutron macromolecular crystallography instrument types |
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9 | (2) |
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11 | (1) |
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6 Planning an experiment with neutrons |
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12 | (1) |
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7 Measuring your diffraction data |
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13 | (1) |
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8 Refining the molecular model against neutron data |
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14 | (1) |
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15 | (1) |
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16 | (1) |
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16 | (1) |
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17 | (1) |
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17 | (2) |
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19 | (2) |
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2 Large crystal growth for neutron protein crystallography |
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21 | (26) |
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22 | (2) |
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2 Crystallization conditions, nucleation, and growth |
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24 | (1) |
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3 Protein solubility and the phase diagram |
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25 | (1) |
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4 Effect of temperature on protein crystallization |
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26 | (2) |
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28 | (14) |
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42 | (1) |
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42 | (1) |
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42 | (5) |
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3 Prospects for membrane protein crystals in NMX |
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47 | (22) |
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Samuel John Hjorth-Jensen |
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Thomas Lykke-Moller Sorensen |
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48 | (2) |
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2 Microdialysis crystallization |
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50 | (5) |
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3 Capillary counter-diffusion crystallization |
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55 | (4) |
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4 Crystallization of SERCA by microdialysis and capillary counterdiffusion |
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59 | (7) |
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66 | (1) |
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67 | (1) |
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67 | (1) |
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67 | (2) |
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4 IMAGINE: The neutron protein crystallography beamline at the high flux isotope reactor |
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69 | (18) |
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70 | (1) |
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71 | (4) |
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3 Sample preparation and ancillary facilities |
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75 | (1) |
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76 | (1) |
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77 | (3) |
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80 | (1) |
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81 | (1) |
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82 | (1) |
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82 | (5) |
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5 The macromolecular neutron diffractometer at the spallation neutron source |
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87 | (14) |
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87 | (4) |
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2 Auto reduction of diffraction data |
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91 | (3) |
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3 Early science highlights |
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94 | (1) |
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4 Human manganese superoxide dismutase |
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94 | (1) |
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95 | (2) |
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97 | (1) |
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98 | (1) |
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98 | (3) |
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6 Current status and near future plan of neutron protein crystallography at J-PARC |
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101 | (24) |
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102 | (1) |
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2 Ibaraki biological crystal diffractometer, iBIX |
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103 | (3) |
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106 | (2) |
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4 Data processing of time-of-fiight diffraction data |
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108 | (3) |
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5 Large protein crystal growth and structure refinements for neutron protein crystallography |
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111 | (2) |
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6 D/H contrast neutron crystallography at iBIX |
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113 | (4) |
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7 New techniques for the detection of hydrogen at a higher sensitivity and future perspectives for neutron sources |
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117 | (4) |
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121 | (1) |
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121 | (1) |
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121 | (4) |
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7 Neutron macromolecular crystallography at the European spallation source |
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125 | (28) |
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1 The European spallation source--Long pulse and high-brilliance moderators |
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126 | (2) |
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2 Implications of the long pulse to instrument design |
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128 | (2) |
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3 The NMX instrument--Design philosophy |
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130 | (2) |
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132 | (14) |
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5 Data collection strategies and optimizing the use of beam time |
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146 | (1) |
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6 Supporting facilities--Deuteration and large crystal growth |
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147 | (1) |
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147 | (3) |
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150 | (1) |
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150 | (3) |
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8 Dynamic nuclear polarization enhanced neutron crystallography: Amplifying hydrogen in biological crystals |
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153 | (24) |
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154 | (4) |
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2 Spin polarized neutron diffraction |
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158 | (4) |
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3 Dynamic nuclear polarization |
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162 | (3) |
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4 DNP apparatus and operation |
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165 | (1) |
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5 DNP-NMC: Polarized neutron diffraction |
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166 | (3) |
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6 Future development and perspectives |
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169 | (2) |
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171 | (1) |
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172 | (1) |
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172 | (3) |
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175 | (2) |
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9 Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix |
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177 | (24) |
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178 | (3) |
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2 Parameterizing the riding hydrogen atom model for typical geometrical configurations |
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181 | (7) |
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3 Riding H: Refinement targets and their gradients |
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188 | (2) |
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4 Constructing the riding H model in CCTBX |
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190 | (2) |
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192 | (1) |
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192 | (1) |
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Appendix. Gradient calculation for riding-H atoms |
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193 | (4) |
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197 | (2) |
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199 | (2) |
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10 Interactive model building in neutron macromolecular crystallography |
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201 | (24) |
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202 | (1) |
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2 Getting started with model building |
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203 | (2) |
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3 Appearance of nuclear density maps |
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205 | (10) |
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4 Interactive model building of neutron crystal structures in Coot |
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215 | (5) |
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5 Depositing a joint X-ray/neutron structure in the Protein Data Bank |
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220 | (1) |
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6 Visualizing nuclear (and electron) density maps in PyMOL |
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221 | (1) |
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222 | (1) |
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223 | (1) |
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223 | (2) |
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11 What are the current limits on determination of protonation state using neutron macromolecular crystallography? |
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225 | (32) |
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226 | (2) |
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228 | (5) |
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233 | (17) |
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250 | (1) |
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251 | (1) |
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251 | (6) |
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12 Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease |
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257 | (24) |
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258 | (3) |
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2 Preparation of PR samples |
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261 | (3) |
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3 Analysis of joint XN structures |
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264 | (12) |
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276 | (1) |
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276 | (1) |
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277 | (4) |
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13 Neutron crystallographic studies of carbonic anhydrase |
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281 | (30) |
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282 | (2) |
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2 X-ray crystallographic studies of carbonic anhydrase |
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284 | (6) |
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3 Neutron crystallography |
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290 | (4) |
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294 | (4) |
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5 Analysis of neutron structures |
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298 | (5) |
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303 | (1) |
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304 | (1) |
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304 | (5) |
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309 | (2) |
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14 Protein kinase A in the neutron beam: Insights for catalysis from directly observing protons |
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311 | (22) |
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312 | (3) |
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2 Protein sample preparation and crystal growth |
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315 | (3) |
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318 | (10) |
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328 | (1) |
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329 | (1) |
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329 | (4) |
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15 Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase |
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333 | (28) |
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334 | (6) |
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2 Catalytic mechanisms and protonation states |
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340 | (5) |
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3 Preparation of large AAT crystals for neutron diffraction |
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345 | (3) |
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4 Data collection, data processing, and structure refinement for AAT |
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348 | (4) |
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5 Using accurate protonation states for computational chemistry methods |
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352 | (4) |
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356 | (5) |
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16 The role of hydrogen atoms in redox catalysis by the flavoenzyme cholesterol oxidase |
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361 | (18) |
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362 | (2) |
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364 | (2) |
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3 Neutron crystallography studies of cholesterol oxidase |
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366 | (7) |
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373 | (1) |
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373 | (6) |
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17 Heme peroxidase--Trapping intermediates by cryo neutron crystallography |
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379 | |
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379 | (2) |
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2 Cryo neutron crystallography |
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381 | (1) |
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382 | (3) |
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4 Neutron structure of compound I of CcP |
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385 | (1) |
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5 Neutron structure of compound II of APX |
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386 | (1) |
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386 | (1) |
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387 | (1) |
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387 | |
Lisainfo e-raamatute kohta