2Q8V
NblA protein from T. vulcanus crystallized with urea
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1OJH |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 25% elthelene glycol, 2M Urea, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.7 | 54.49 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 43.265 | α = 90 |
b = 43.265 | β = 90 |
c = 149.4 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 32 2 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 | CCD | ADSC QUANTUM 4 | M | SINGLE WAVELENGTH | |||||||
2 | 1 | x-ray | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.97913 | ESRF | BM30A |
2 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.9792 | ESRF | ID14-1 |
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 | 2.5 | 50 | 99.8 | 0.073 | 19.1 | 6.2 | 6108 | 2.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.5 | 2.64 | 100 | 0.326 | 0.358 | 4.4 | 5.9 | 849 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD/Molecular Replacement | THROUGHOUT | 1OJH | 2.5 | 30 | 6108 | 984 | 100 | 0.245 | 0.264 | random | 36.4 |
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] | |
-6.085 | -7.701 | -6.085 | 12.17 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 20.2 |
c_improper_angle_d | 1.72 |
c_angle_deg | 1.09 |
c_bond_d | 0.0096 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 843 |
Nucleic Acid Atoms | |
Solvent Atoms | 16 |
Heterogen Atoms | 8 |
Software
Software | |
---|---|
Software Name | Purpose |
DNA | data collection |
CCP4 | model building |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
CCP4 | phasing |