6PRC
PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (DG-420314 (TRIAZINE) COMPLEX)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2PRC | PDB ENTRY 2PRC |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6 | pH 6.0 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
4.9 | 70 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 223.5 | α = 90 |
b = 223.5 | β = 90 |
c = 113.6 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 263 | IMAGE PLATE | MARRESEARCH | TOROIDAL MIRROR | 1993-08-06 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MPG/DESY, HAMBURG BEAMLINE BW6 | MPG/DESY, HAMBURG | BW6 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.3 | 30 | 81 | 0.073 | 0.073 | 9.1 | 2.5 | 102956 | 1.5 |
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) | ||||||||||
1 | 2.3 | 2.36 | 51.8 | 0.247 | 0.247 | 2.7 | 1.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | DIFFERENCE FOURIER / SA OMIT MAPS | A POSTERIORI | PDB ENTRY 2PRC | 2.3 | 10 | 1.5 | 102117 | 10277 | 81.4 | 0.184 | 0.184 | 0.225 | RANDOM | 32.6 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 23.7 |
x_scangle_it | 2.5 |
x_improper_angle_d | 2.14 |
x_mcangle_it | 2 |
x_scbond_it | 2 |
x_mcbond_it | 1.5 |
x_angle_deg | 1.37 |
x_bond_d | 0.011 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 9342 |
Nucleic Acid Atoms | |
Solvent Atoms | 337 |
Heterogen Atoms | 788 |
Software
Software | |
---|---|
Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
Agrovata | data scaling |
X-PLOR | phasing |