4WAV
Crystal Structure of Haloquadratum walsbyi bacteriorhodopsin mutant D93N
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VGO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 7 | 293 | calcium chloride, HEPES, PEG 400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 29.86 | α = 90 |
b = 131.942 | β = 90 |
c = 235.423 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||||||||||||||||
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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 | |
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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 |