3M98
Crystal structure of human carbonic anhydrase isozyme II with 5-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3HLJ | PDB entry 3HLJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | Crystallization buffer was 0.1M sodium BICINE, pH 9.0, 0.2 M ammonium sulfate and 2M sodium malonate, pH 7.0 made from 1M sodium BICINE and 3.4M sodium malonate, vapor diffusion, sitting drop, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.233 | α = 90 |
b = 41.112 | β = 104.05 |
c = 72.109 | 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 | CCD | MAR CCD 165 mm | 2009-12-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.8120 | EMBL/DESY, HAMBURG | X13 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.5 | 39.81 | 98 | 0.045 | 0.045 | 35.9 | 9.9 | 37890 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.5 | 1.58 | 97.1 | 0.324 | 0.324 | 6 | 9.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 3HLJ | 1.5 | 39.81 | 38726 | 34084 | 3806 | 97.84 | 0.13976 | 0.13479 | 0.184 | RANDOM | 16.463 |
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] | |
-0.06 | 0.04 | -0.03 | 0.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.237 |
r_dihedral_angle_4_deg | 23.93 |
r_sphericity_free | 13.164 |
r_dihedral_angle_3_deg | 12.66 |
r_sphericity_bonded | 7.872 |
r_scangle_it | 6.55 |
r_dihedral_angle_1_deg | 6.344 |
r_scbond_it | 4.887 |
r_mcangle_it | 3.685 |
r_rigid_bond_restr | 3.029 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2049 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MAR345 | data collection |