4UAT
Crystal structure of CbbY (mutant D10N) from Rhodobacter sphaeroides in complex with Xylulose-(1,5)bisphosphate, crystal form I
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | 25 % PEG-550MME, 0.1 M MES-NaOH pH 6.5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.21 | 44.26 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 35.419 | α = 90 |
b = 51.468 | β = 94.06 |
c = 122.083 | 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 | PIXEL | DECTRIS PILATUS 2M | 2013-05-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.97639 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.3 | 121.776 | 99.5 | 0.066 | 0.074 | 0.033 | 13.2 | 4.7 | 107256 | 107256 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.3 | 1.37 | 97.4 | 0.839 | 0.839 | 0.451 | 0.9 | 4.2 | 15268 |
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 | PDB entry 4UAR | 1.3 | 30 | 107186 | 5342 | 99.43 | 0.1235 | 0.1212 | 0.1685 | RANDOM | 16.916 |
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] | |
1.07 | -0.2 | -0.26 | -0.79 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_sphericity_free | 35.806 |
r_dihedral_angle_2_deg | 30.413 |
r_dihedral_angle_4_deg | 19.755 |
r_dihedral_angle_3_deg | 13.018 |
r_sphericity_bonded | 11.348 |
r_dihedral_angle_1_deg | 6.244 |
r_rigid_bond_restr | 6.034 |
r_angle_refined_deg | 2.049 |
r_angle_other_deg | 0.955 |
r_chiral_restr | 0.249 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3466 |
Nucleic Acid Atoms | |
Solvent Atoms | 661 |
Heterogen Atoms | 62 |
Software
Software | |
---|---|
Software Name | Purpose |
SCALA | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
REFMAC | refinement |
XSCALE | data reduction |