6F3B
Crystal structure of human carbonic anhydrase I in complex with the 1-(2-hydroxy-5-sulfamoylphenyl)-3-[(4-methylphenyl)methyl]urea inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JV0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 296 | 28% PEG4000, 0.2 M Sodium acetate, Tris 100 mM |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 47.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.375 | α = 90 |
b = 71.229 | β = 90 |
c = 120.871 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2016-12-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.973 | ESRF | ID30B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.4 | 61.37 | 98.4 | 0.057 | 0.065 | 0.999 | 10.87 | 4.234 | 105665 | 24.149 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.4 | 1.48 | 97.6 | 0.54 | 0.618 | 0.317 | 2.11 | 4.134 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 1jv0 | 1.4 | 61.37 | 99794 | 5336 | 98.66 | 0.21056 | 0.20867 | 0.24579 | RANDOM | 24.911 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.78 | 1.63 | -0.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.95 |
r_dihedral_angle_4_deg | 18.51 |
r_dihedral_angle_3_deg | 12.293 |
r_dihedral_angle_1_deg | 6.467 |
r_long_range_B_refined | 5.073 |
r_mcangle_it | 2.059 |
r_scbond_it | 1.837 |
r_angle_refined_deg | 1.373 |
r_mcbond_it | 1.333 |
r_chiral_restr | 0.095 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4016 |
Nucleic Acid Atoms | |
Solvent Atoms | 517 |
Heterogen Atoms | 74 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
MxCuBE | data collection |