2F2U
crystal structure of the Rho-kinase kinase domain
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1APM | PDB ENTRY 1APM |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5 | 298 | 0.8M Sodium Citrate, 0.1M Sodium Citrate Buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.76 | 67.31 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 102.531 | α = 90 |
| b = 102.531 | β = 90 |
| c = 257.185 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 90 | CCD | Bruker DIP-6040 | a double-crystal monochromator and a horizontal focusing mirror | 2003-04-20 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9 | SPring-8 | BL44XU |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.4 | 30 | 95.8 | 0.075 | 53814 | 52492 | |||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 2.4 | 2.49 | 81 | 0.347 | ||||||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1APM | 2.4 | 30 | 52481 | 52481 | 2663 | 95.92 | 0.197 | 0.197 | 0.195 | 0.235 | RANDOM | 47.404 | ||||
| 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] | |
| 0.19 | 0.19 | -0.38 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.593 |
| r_dihedral_angle_4_deg | 23.701 |
| r_dihedral_angle_3_deg | 15.077 |
| r_scangle_it | 6.071 |
| r_scbond_it | 3.866 |
| r_mcangle_it | 2.547 |
| r_dihedral_angle_1_deg | 2.384 |
| r_angle_refined_deg | 1.681 |
| r_mcbond_it | 1.348 |
| r_nbtor_refined | 0.324 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6211 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 162 |
| Heterogen Atoms | 40 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
