2R4H
Crystal structure of a C1190S mutant of the 6th PDZ domain of human membrane associated guanylate kinase
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 277 | 20% PEG 3350, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.99 | 38.18 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 40.052 | α = 90 |
| b = 77.759 | β = 101.49 |
| c = 50.182 | 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 | MARMOSAIC 225 mm CCD | 2007-07-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.006029 | SLS | X10SA |
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 | 2.05 | 39.25 | 92.6 | 0.133 | 0.133 | 9.1 | 3.1 | 17538 | 17538 | 22.2 | |||||||||
| 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 | 2.05 | 2.16 | 99.8 | 0.683 | 0.683 | 2.1 | 3.1 | 8383 | |||||||||||
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 2JIK | 2.05 | 38.87 | 16559 | 16559 | 883 | 91.82 | 0.19148 | 0.19148 | 0.18781 | 0.25829 | RANDOM | 16.086 | ||||
| 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] | |
| 0.33 | 0.13 | -0.12 | -0.15 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.629 |
| r_dihedral_angle_4_deg | 18.747 |
| r_dihedral_angle_3_deg | 17.744 |
| r_scangle_it | 10.191 |
| r_scbond_it | 7.918 |
| r_dihedral_angle_1_deg | 6.252 |
| r_mcangle_it | 5.773 |
| r_mcbond_it | 5.197 |
| r_mcbond_other | 2.263 |
| r_angle_refined_deg | 1.683 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2091 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 114 |
| Heterogen Atoms | 50 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MAR345 | data collection |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
