3SBI
Crystal structure of human carbonic anhydrase isozyme II with 4-[(2-pyrimidinylsulfanyl)acetyl]benzenesulfonamide
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3HLJ | PDB entry 3HLJ |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 9 | 293 | 0.1M Na-bicine pH 9, 2M Na-malonate pH 7.55, VAPOR DIFFUSION, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.1 | 41.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.348 | α = 90 |
| b = 41.314 | β = 104.25 |
| c = 72.24 | 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 | CCD | MAR CCD 165 mm | Bent, vertically focussing mirrors | 2010-11-12 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.8123 | EMBL/DESY, HAMBURG | X13 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.4 | 20.68 | 97.1 | 0.043 | 0.043 | 25.2 | 6 | 46467 | 12.4 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.4 | 1.48 | 95.7 | 0.344 | 0.344 | 2 | 6 | 6675 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MR | THROUGHOUT | PDB entry 3HLJ | 1.4 | 20.66 | 46451 | 46451 | 4705 | 96.88 | 0.138 | 0.138 | 0.133 | 0.183 | RANDOM | 14.597 | ||||
| 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] | |
| 0.21 | -0.05 | -0.19 | -0.04 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.908 |
| r_dihedral_angle_4_deg | 22.742 |
| r_sphericity_free | 13.699 |
| r_dihedral_angle_3_deg | 12.767 |
| r_sphericity_bonded | 7.853 |
| r_dihedral_angle_1_deg | 6.795 |
| r_scangle_it | 5.924 |
| r_scbond_it | 4.662 |
| r_mcangle_it | 3.637 |
| r_rigid_bond_restr | 3.065 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2059 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 320 |
| Heterogen Atoms | 40 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| DNA | data collection |
