Crystal structure of carbonic anhydrase II with N-butyl-4-chloro-3-sulfamoyl-benzamide
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4HT0 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 291 | 0.1M sodium bicine (pH 9) and 2M sodium malonate (pH 7) | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2 | 38.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.025 | α = 90 |
| b = 41.066 | β = 104.22 |
| c = 71.906 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2018-11-22 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 1.033200 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.12 | 69.7 | 96 | 0.046 | 0.057 | 0.022 | 0.998 | 13.7 | 6.6 | 87594 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.12 | 1.18 | 91.3 | 0.309 | 0.372 | 0.149 | 0.92 | 6 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.12 | 40.74 | 78781 | 8712 | 95.61 | 0.14818 | 0.14523 | 0.1558 | 0.17378 | 0.1777 | RANDOM | 19.597 | |||||
| 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] | |
| -1.62 | -0.17 | 0.62 | 0.96 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.747 |
| r_sphericity_free | 30.248 |
| r_sphericity_bonded | 24.86 |
| r_dihedral_angle_4_deg | 18.87 |
| r_rigid_bond_restr | 15.319 |
| r_dihedral_angle_3_deg | 13.769 |
| r_scbond_it | 9.785 |
| r_dihedral_angle_1_deg | 7.299 |
| r_long_range_B_refined | 7.253 |
| r_mcbond_it | 5.332 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2042 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 266 |
| Heterogen Atoms | 35 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SCALA | data scaling |
| Coot | model building |
| MOLREP | phasing |
| XDS | data reduction |
