4HBH

Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides with ILE M265 replaced with ASN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PCRPDB ENTRY 1PCR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298drop: 13 mg/mL protein, 0.8 M potassium phosphate, 5 mM Tris, 5 uM EDTA, 4.0% 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 298K
Crystal Properties
Matthews coefficientSolvent content
5.6878.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.72α = 90
b = 139.72β = 90
c = 183.98γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-GAPS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.93121.00199.60.12513.3745001-355.99
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.933.011000.7932.89

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1PCR2.9312144997225099.60.1870.1850.22648.49
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]
-0.03-0.01-0.030.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.199
r_dihedral_angle_4_deg23.924
r_dihedral_angle_3_deg21.08
r_dihedral_angle_1_deg7.376
r_scangle_it3.655
r_angle_refined_deg2.364
r_scbond_it2.306
r_mcangle_it1.558
r_mcbond_it0.806
r_chiral_restr0.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.199
r_dihedral_angle_4_deg23.924
r_dihedral_angle_3_deg21.08
r_dihedral_angle_1_deg7.376
r_scangle_it3.655
r_angle_refined_deg2.364
r_scbond_it2.306
r_mcangle_it1.558
r_mcbond_it0.806
r_chiral_restr0.138
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6391
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms507

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
XSCALEdata scaling