2UX5

X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 9 in the charge-separated state


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
19pH 9
Crystal Properties
Matthews coefficientSolvent content
4.8174.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.46α = 90
b = 139.46β = 90
c = 184.73γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2003-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
12.25098.10.110.292.5103587-3
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)
12.22.389.20.433.721.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PCR2.2150100374311099.10.2030.2020.236RANDOM43.65
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
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.008
r_scangle_it3.725
r_scbond_it2.529
r_angle_refined_deg2.465
r_mcangle_it1.714
r_mcbond_it0.959
r_nbd_refined0.218
r_symmetry_hbond_refined0.21
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.008
r_scangle_it3.725
r_scbond_it2.529
r_angle_refined_deg2.465
r_mcangle_it1.714
r_mcbond_it0.959
r_nbd_refined0.218
r_symmetry_hbond_refined0.21
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.167
r_chiral_restr0.126
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6471
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms790

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing