CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH SALVIANOLIC ACID P
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4XE1 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 1.3 M sodium citrate, 60 mM Tris-HCl |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.06 | 40.42 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.222 | α = 90 |
| b = 41.268 | β = 104.37 |
| c = 72.101 | 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 | RIGAKU HyPix-6000HE | 2023-05-10 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU PhotonJet-R | 1.54178 | ||
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 | 1.2 | 34.95 | 91.3 | 0.053 | 0.063 | 0.033 | 0.998 | 24.1 | 2.7 | 68762 | |||||||||
| 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 | 1.2 | 1.22 | 86.7 | 0.201 | 0.258 | 0.16 | 0.914 | 2 | |||||||||||
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 | FOURIER SYNTHESIS | FREE R-VALUE | 1.2 | 34.95 | 66677 | 2070 | 91.24 | 0.13588 | 0.13525 | 0.1443 | 0.15671 | 0.1621 | RANDOM | 9.926 | |||||
| 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 | -0.09 | 0.14 | -0.04 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 11.827 |
| r_dihedral_angle_1_deg | 6.938 |
| r_dihedral_angle_2_deg | 6.103 |
| r_long_range_B_refined | 6.038 |
| r_long_range_B_other | 5.996 |
| r_scangle_other | 4.524 |
| r_rigid_bond_restr | 3.748 |
| r_mcangle_other | 3.698 |
| r_mcangle_it | 3.694 |
| r_scbond_it | 2.882 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2048 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 258 |
| Heterogen Atoms | 46 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SCALEPACK | data scaling |
| HKL-3000 | data reduction |
| REFMAC | phasing |
