2UXJ

X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 10 in the neutral state


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110pH 10
Crystal Properties
Matthews coefficientSolvent content
5.2976.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.376α = 90
b = 139.376β = 90
c = 235.041γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2002-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
12.253093.90.0729.24.4103927-3
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)
12.252.2876.70.343.08

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 1PCR2.25119.52981645178940.1950.1940.225RANDOM48.87
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_deg5.684
r_scangle_it3.236
r_angle_refined_deg2.367
r_scbond_it2.1
r_mcangle_it1.442
r_mcbond_it0.771
r_symmetry_vdw_refined0.323
r_nbd_refined0.209
r_xyhbond_nbd_refined0.171
r_symmetry_hbond_refined0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.684
r_scangle_it3.236
r_angle_refined_deg2.367
r_scbond_it2.1
r_mcangle_it1.442
r_mcbond_it0.771
r_symmetry_vdw_refined0.323
r_nbd_refined0.209
r_xyhbond_nbd_refined0.171
r_symmetry_hbond_refined0.105
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.006
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 Atoms403
Heterogen Atoms794

Software

Software
Software NamePurpose
REFMACrefinement
HKLdata reduction
SCALEPACKdata scaling
CNSphasing