6QN2
Three dimensional structure of human carbonic anhydrase IX in complex with benzenesulfonamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6FE2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 294 | CRYSTALLIZATION CONDITIONS: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.46 | 64.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 152.64 | α = 90 |
b = 152.64 | β = 90 |
c = 172.84 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 EIGER X 16M | 2018-10-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX IV BEAMLINE BioMAX | 0.97776 | MAX IV | BioMAX |
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 | 1.95 | 76.32 | 100 | 0.145 | 6.2 | 5.2 | 109432 | 36.116 |
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 | 1.95 | 2.06 | 100 | 0.581 | 2.6 | 5.2 |
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 | 6FE2 | 1.95 | 76.32 | 103914 | 5517 | 100 | 0.21481 | 0.21278 | 0.25328 | RANDOM | 38.237 |
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] | |
0.11 | 0.06 | 0.11 | -0.37 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.763 |
r_dihedral_angle_4_deg | 19.646 |
r_dihedral_angle_3_deg | 15.464 |
r_long_range_B_refined | 7.982 |
r_long_range_B_other | 7.959 |
r_dihedral_angle_1_deg | 7.381 |
r_scangle_other | 5.879 |
r_mcangle_it | 4.801 |
r_mcangle_other | 4.8 |
r_scbond_it | 3.901 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7729 |
Nucleic Acid Atoms | |
Solvent Atoms | 638 |
Heterogen Atoms | 116 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |