5MJN
Three dimensional structure of human carbonic anhydrase II in complex with 5-[(4Chlorobenzyl)sulfanyl]thiophene-2-sulfonamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4BF1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 294 | 1,54 M SODIUM CITRATE 60 MM TRIS- HCL, PH 9.0, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, TIME 2-5 DAYS |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.36 | α = 90 |
b = 41.32 | β = 104.48 |
c = 72.25 | 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 | MARRESEARCH | MULTILAYER | 2013-11-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-3 | 0.97671 | MAX II | I911-3 |
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 | 1.17 | 18 | 99.6 | 0.098 | 6.3 | 3.3 | 81743 | 2 | 6.4 |
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 | 1.17 | 1.23 | 98.3 | 0.452 | 2.3 | 3 |
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 | 4BF1 | 1.17 | 18 | 77608 | 3989 | 99.29 | 0.14152 | 0.13989 | 0.17349 | RANDOM | 16.697 |
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] | |
0.33 | 1.73 | 0.53 | -1.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 40.548 |
r_dihedral_angle_2_deg | 37.288 |
r_rigid_bond_restr | 27.547 |
r_dihedral_angle_4_deg | 23.855 |
r_sphericity_bonded | 17.125 |
r_dihedral_angle_3_deg | 11.238 |
r_scangle_other | 9.123 |
r_long_range_B_refined | 8.54 |
r_long_range_B_other | 8.36 |
r_scbond_it | 7.892 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2040 |
Nucleic Acid Atoms | |
Solvent Atoms | 319 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Coot | model building |