4H9L
Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides with ILE M265 replaced with SER
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1PCR | PDB ENTRY 1PCR |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | drop: 14 mg/mL protein, 0.8 M potassium phosphate, 5 mM Tris, 5 uM EDTA, 3.2% 1,2,3-heptanetriol, 2.0% dioxane, 140 mM sodium chloride, 0.045% LDAO, reservoir: 1.6 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
5.74 | 78.57 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 140.19 | α = 90 |
b = 140.19 | β = 90 |
c = 184.56 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 31 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 | MARMOSAIC 300 mm CCD | 2011-07-29 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | APS | 21-ID-D |
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 | 2.77 | 121.408 | 99.5 | 0.105 | 11.77 | 53634 | -3 | 59.93 |
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 | 2.77 | 2.84 | 100 | 0.775 | 2.14 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1PCR | 2.77 | 19.9 | 53634 | 2682 | 99.9 | 0.192 | 0.191 | 0.227 | 50 |
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] | |
0.25 | 0.13 | 0.25 | -0.38 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.856 |
r_dihedral_angle_4_deg | 25.251 |
r_dihedral_angle_3_deg | 20.015 |
r_dihedral_angle_1_deg | 7.406 |
r_scangle_it | 4.044 |
r_scbond_it | 2.639 |
r_angle_refined_deg | 2.58 |
r_mcangle_it | 1.685 |
r_mcbond_it | 0.91 |
r_chiral_restr | 0.148 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6356 |
Nucleic Acid Atoms | |
Solvent Atoms | 98 |
Heterogen Atoms | 462 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
REFMAC | phasing |
XSCALE | data scaling |