4WAV
Crystal Structure of Haloquadratum walsbyi bacteriorhodopsin mutant D93N
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | LIPIDIC CUBIC PHASE | 7 | 293 | calcium chloride, HEPES, PEG 400 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.03 | 39.52 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 29.86 | α = 90 |
| b = 131.942 | β = 90 |
| c = 235.423 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 110 | CCD | RAYONIX MX300HE | Inter-Frame | 2013-08-03 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | OTHER | 1.000 | NSRRC | BL15A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.8 | 30 | 97.2 | 0.149 | 5.7 | 6.1 | 11796 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.8 | 2.85 | 98 | 0.972 | 6.2 | 599 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 1VGO | 2.8 | 26.12 | 9924 | 504 | 86.16 | 0.1844 | 0.1816 | 0.2392 | RANDOM | 27.78 | ||||||
| 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] | |
| 2.06 | 0.29 | -2.35 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.354 |
| r_dihedral_angle_3_deg | 23.146 |
| r_dihedral_angle_4_deg | 17.911 |
| r_dihedral_angle_1_deg | 5.405 |
| r_angle_refined_deg | 1.514 |
| r_angle_other_deg | 0.909 |
| r_chiral_restr | 0.085 |
| r_bond_refined_d | 0.012 |
| r_gen_planes_refined | 0.007 |
| r_gen_planes_other | 0.005 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3494 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 160 |
| Heterogen Atoms | 88 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Blu-Ice | data reduction |
| MOLREP | phasing |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data scaling |
| HKL | data reduction |
| HKL | data scaling |
