4UAS
Crystal structure of CbbY from Rhodobacter sphaeroides in complex with phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4UAR | PDB entry 4UAR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 10 mM fructose-1,6-bisphosphate, 22 % PEG-6000 and 0.1 M MES-HCl pH 6.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.805 | α = 90 |
b = 70.885 | β = 90 |
c = 125.433 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2012-05-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.99987 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.2 | 46.971 | 97.8 | 0.048 | 0.054 | 0.025 | 12.2 | 4.3 | 142564 | 142564 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.2 | 1.26 | 91.2 | 0.612 | 0.612 | 0.34 | 1.3 | 3.9 | 19182 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB entry 4UAR | 1.2 | 20 | 142115 | 7161 | 98.19 | 0.1367 | 0.1348 | 0.1734 | RANDOM | 17.175 |
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] | |
-0.11 | 0.33 | -0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 47.29 |
r_dihedral_angle_2_deg | 31.089 |
r_dihedral_angle_4_deg | 17.943 |
r_sphericity_bonded | 13.517 |
r_dihedral_angle_3_deg | 12.625 |
r_dihedral_angle_1_deg | 6.248 |
r_rigid_bond_restr | 5.252 |
r_angle_refined_deg | 1.967 |
r_angle_other_deg | 1.253 |
r_chiral_restr | 0.369 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3476 |
Nucleic Acid Atoms | |
Solvent Atoms | 832 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data reduction |