5ZE6
CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-981
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3WJK |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 298 | 0.3M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1M TRIS-HCL, 24%(W/V) POLYETHYLENE GLYCOL 3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.61 | 52.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.032 | α = 90 |
b = 111.999 | β = 90 |
c = 133.822 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 315r | 2012-08-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE BL13B1 | 1.0 | NSRRC | BL13B1 |
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 | 2.5 | 25 | 100 | 0.097 | 9.4 | 5.8 | 49730 |
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 | 2.5 | 2.59 | 100 | 0.495 | 5.9 |
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 | 3WJK | 2.5 | 25 | 47239 | 2427 | 99.63 | 0.18931 | 0.18544 | 0.26405 | RANDOM | 41.108 |
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] | |
0.21 | 1.3 | -1.51 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.367 |
r_dihedral_angle_4_deg | 23.383 |
r_dihedral_angle_3_deg | 22.361 |
r_long_range_B_other | 9.596 |
r_long_range_B_refined | 9.593 |
r_scangle_other | 6.611 |
r_dihedral_angle_1_deg | 5.756 |
r_mcangle_it | 5.464 |
r_mcangle_other | 5.464 |
r_scbond_it | 4.438 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 9411 |
Nucleic Acid Atoms | |
Solvent Atoms | 417 |
Heterogen Atoms | 52 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |