4AXB
Crystal structure of soman-aged human butyrylcholinesterase in complex with 2-PAM
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1P0I | PDB ENTRY 1P0I |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.4 | PROTEIN WAS CRYSTALLIZED FROM 2.1 M AMMONIUM SULFATE, 100 MM MES BUFFER PH 6.5. THEN SOAKED IN 20% GLYCEROL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.09 | 60.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 155.95 | α = 90 |
b = 155.95 | β = 90 |
c = 127.9 | γ = 90 |
Symmetry | |
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Space Group | I 4 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 63 | CCD | MARMOSAIC 225 mm CCD | 2010-02-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | ||||||||
1 | 2.4 | 110.27 | 99.7 | 0.09 | 15.6 | 8.8 | 29874 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.4 | 2.55 | 99.8 | 0.34 | 5.2 | 9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1P0I | 2.4 | 110.27 | 29428 | 1563 | 99.55 | 0.1707 | 0.16808 | 0.22117 | RANDOM | 38.713 |
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] | |
0.27 | 0.27 | -0.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.941 |
r_dihedral_angle_4_deg | 17.911 |
r_dihedral_angle_3_deg | 16.86 |
r_dihedral_angle_1_deg | 7.099 |
r_scangle_it | 5.261 |
r_scbond_it | 3.31 |
r_mcangle_it | 2.045 |
r_angle_refined_deg | 1.998 |
r_mcbond_it | 1.122 |
r_chiral_restr | 0.14 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4207 |
Nucleic Acid Atoms | |
Solvent Atoms | 356 |
Heterogen Atoms | 175 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |