4WW8
Crystal structure of human carbonic anhydrase isozyme XII with 4-Propylthiobenzenesulfonamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JD0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 291 | Crystallization buffer: 0.1M ammonium citrate (pH 7.0), 0.2M ammonium sulfate and 30% PEG4000. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.313 | α = 90 |
b = 74.26 | β = 108.66 |
c = 91.57 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 2014-01-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.826606 | 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 | 1.42 | 74.26 | 95.8 | 0.054 | 0.064 | 0.024 | 16.7 | 6.7 | 176873 | 176873 |
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 | 1.42 | 1.5 | 79 | 0.37 | 0.37 | 0.45 | 0.19 | 2 | 5.6 | 21090 |
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 | 1JD0 | 1.42 | 56.42 | 176847 | 17544 | 95.7 | 0.175 | 0.172 | 0.205 | RANDOM | 18.976 |
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] | |
-0.4 | 0.24 | 0.31 | 0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.784 |
r_dihedral_angle_4_deg | 16.09 |
r_dihedral_angle_3_deg | 12.229 |
r_dihedral_angle_1_deg | 7.03 |
r_angle_refined_deg | 2.27 |
r_chiral_restr | 0.173 |
r_bond_refined_d | 0.024 |
r_gen_planes_refined | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8380 |
Nucleic Acid Atoms | |
Solvent Atoms | 912 |
Heterogen Atoms | 112 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
PDB_EXTRACT | data extraction |
SCALA | data scaling |
REFMAC | refinement |
Coot | model building |
MOLREP | phasing |