4H1T
X-RAY Structure of the Complex VchUPh with Phosphate ion at 1.92A Resolution.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3O6V |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 292 | 0.1 M Ammonium sulfate 0.5 M di-Sodium phosphate 0.5 M di-Potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.19 | 43.77 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 63.691 | α = 69.62 |
b = 71.08 | β = 72.56 |
c = 87.937 | γ = 85.74 |
Symmetry | |
---|---|
Space Group | P 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 | MAR CCD 165 mm | 2012-05-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.81 | EMBL/DESY, HAMBURG | X13 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.924 | 78.817 | 98.3 | 0.037 | 30 | 3.9 | 102754 | 102754 | 10.747 |
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) | ||||||||||
1 | 1.92 | 2.03 | 96.3 | 0.111 | 0.111 | 7 | 3.7 | 14647 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 3O6V | 1.924 | 26.272 | 1.97 | 103696 | 102659 | 5129 | 98.24 | 0.1812 | 0.1791 | 0.1771 | 0.2171 | RANDOM | 13.4436 |
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] | |
0.0479 | -0.0825 | -0.0778 | -0.1072 | 0.0373 | 0.0593 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.761 |
f_angle_d | 0.843 |
f_chiral_restr | 0.056 |
f_bond_d | 0.008 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 11257 |
Nucleic Acid Atoms | |
Solvent Atoms | 1230 |
Heterogen Atoms | 445 |
Software
Software | |
---|---|
Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MAR345dtb | data collection |
XDS | data reduction |