5OGJ
Crystal structure of human carbonic anhydrase isozyme XIII with 2-(Cyclooctylamino)-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4HU1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 5 | 291 | Crystallization buffer: 0.1M ammonium citrate (pH 7), 0.1M sodium acetate (pH 4.5) and 26% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.445 | α = 90 |
b = 57.244 | β = 90 |
c = 159.782 | 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 | 2013-05-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.976300 | PETRA III, EMBL c/o DESY | P14 (MX2) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (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 | ||||||
1 | 1.06 | 79.891 | 98.6 | 0.042 | 0.052 | 0.021 | 18.4 | 6 | 229112 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.063 | 1.12 | 90.9 | 0.324 | 0.324 | 0.421 | 0.202 | 2.2 | 4 |
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 | 4HU1 | 1.06 | 79.89 | 206280 | 22703 | 98.58 | 0.1343 | 0.132 | 0.155 | RANDOM | 15.406 |
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] | |
-0.05 | 0.04 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.04 |
r_sphericity_free | 28.069 |
r_dihedral_angle_4_deg | 15.825 |
r_sphericity_bonded | 14.014 |
r_dihedral_angle_3_deg | 11.934 |
r_rigid_bond_restr | 9.832 |
r_dihedral_angle_1_deg | 7.012 |
r_angle_refined_deg | 2.37 |
r_chiral_restr | 0.173 |
r_bond_refined_d | 0.024 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4157 |
Nucleic Acid Atoms | |
Solvent Atoms | 714 |
Heterogen Atoms | 141 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
MOLREP | phasing |