6RG4
Crystal structure of human Carbonic anhydrase II in complex with (R)-4-(2-benzyl-4-methylpiperazin-1-yl)benzenesulfonamide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.3 | 286 | 1.6 sodium citrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.37 | α = 90 |
b = 41.299 | β = 104.38 |
c = 71.936 | 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 PILATUS3 S 6M | 2018-03-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.827 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.25 | 41.08 | 99.1 | 0.058 | 0.069 | 0.998 | 9.39 | 3.332 | 66147 | 21.135 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.25 | 1.33 | 99.1 | 0.992 | 1.189 | 0.541 | 0.79 | 3.227 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 4FIK | 1.25 | 41.08 | 62531 | 3239 | 98.4 | 0.1577 | 0.1556 | 0.2002 | RANDOM | 18.175 |
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 | -0.31 | 0.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.275 |
r_dihedral_angle_4_deg | 25.003 |
r_dihedral_angle_3_deg | 13.018 |
r_dihedral_angle_1_deg | 7.163 |
r_rigid_bond_restr | 3.708 |
r_angle_refined_deg | 2.008 |
r_angle_other_deg | 1.527 |
r_chiral_restr | 0.11 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2059 |
Nucleic Acid Atoms | |
Solvent Atoms | 279 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
REFMAC | phasing |