4E04
RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.5 | 18% PEG3350, 0.2 mM MgCl2 or 0.2 mM CaCl2 and 0.1 Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.16 | 43.17 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 52.35 | α = 90 |
| b = 79.86 | β = 90 |
| c = 149.88 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | PSI PILATUS 6M | 2010-08-03 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 | |
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 | 1.79 | 74.8 | 99.8 | 0.023 | 24.9 | 4.3 | 59311 | ||||||||||||
| 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) | |||||||||||
| 1 | 1.79 | 1.84 | 99.5 | 0.537 | 2.3 | 4.3 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.79 | 15 | 56814 | 3027 | 99.7 | 0.184 | 0.181 | 0.232 | RANDOM | 50.84 | |||||||
| 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 | 0.69 | -0.89 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.606 |
| r_dihedral_angle_4_deg | 20.43 |
| r_dihedral_angle_3_deg | 15.673 |
| r_dihedral_angle_1_deg | 7.316 |
| r_scangle_it | 4.893 |
| r_scbond_it | 3.135 |
| r_angle_refined_deg | 2.359 |
| r_mcangle_it | 2.153 |
| r_mcbond_it | 1.259 |
| r_mcbond_other | 0.386 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4786 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 515 |
| Heterogen Atoms | 86 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| xia2 | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
