Joint X-ray/neutron structure of cationic trypsin in complex with benzylamine
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 15.0-16.5% (w/v) PEG 8000 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.32 | 47.08 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 54.841 | α = 90 |
b = 58.334 | β = 90 |
c = 67.781 | γ = 90 |
Symmetry |
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Space Group | P 21 21 21 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 295 | PIXEL | DECTRIS PILATUS 6M | | 2015-06-10 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 295 | IMAGE PLATE | MAATEL BIODIFF | | 2016-08-10 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.8266 | PETRA III, EMBL c/o DESY | P14 (MX2) |
2 | NUCLEAR REACTOR | FRM II BEAMLINE BIODIFF | 2.673 | FRM II | BIODIFF |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
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1 | 0.98 | 44.215 | 99.6 | 0.052 | | | | | | 19.99 | 6.403 | | 124579 | | | |
2 | 1.49 | 50 | 93.7 | 0.129 | | | | | | 5.866 | 2.8 | | 34022 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 0.98 | 1.04 | | 0.562 | | | | | | 4.18 | 6.184 | |
2 | 1.49 | 1.52 | | 0.445 | | | | | | 1.954 | 2.1 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 0.98 | 17.437 | | 1.36 | | 124484 | 6242 | 99.61 | | 0.0999 | 0.0995 | 0.1077 | Random selection | |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.49 | 19.667 | | | | 34004 | 1713 | 93.67 | | 0.1968 | 0.1962 | 0.2074 | Random selection | |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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| | | | | |
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RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 14.535 |
f_dihedral_angle_d | 14.535 |
f_angle_d | 1.261 |
f_angle_d | 1.261 |
f_chiral_restr | 0.098 |
f_chiral_restr | 0.098 |
f_plane_restr | 0.008 |
f_plane_restr | 0.008 |
f_bond_d | 0.006 |
f_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1613 |
Nucleic Acid Atoms | |
Solvent Atoms | 146 |
Heterogen Atoms | 24 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
XDS | data reduction |
HKL-2000 | data reduction |
XDS | data scaling |
HKL-2000 | data scaling |
PHASER | phasing |
Coot | model building |