2WX5

Hexa-coordination of a bacteriochlorophyll cofactor in the Rhodobacter sphaeroides reaction centre


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AIGPDB ENTRY 1AIG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18MOTHER LIQUOR AT 9 MG/ML OF THE AM149W REACTION CENTRE, 0.09% V/V LDAO, 3.5% W/V HEPTANE-1, 2,3-TRIOL AND 0.65 M POTASSIUM PHOSPHATE (PH 8.0) WERE EQUILIBRATED AGAINST A RESERVOIR SOLUTION OF 1.5 M POTASSIUM PHOSPHATE
Crystal Properties
Matthews coefficientSolvent content
5.678

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.18α = 90
b = 140.18β = 90
c = 185.401γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002004-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.1SRSPX14.1

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
12.6344.5498.60.18.24.961876
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)
12.632.7894.90.71.54.1

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 1AIG2.6320.458556312698.490.239410.237280.27866RANDOM68.291
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]
1.290.641.29-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.59
r_dihedral_angle_4_deg21.238
r_dihedral_angle_3_deg18.394
r_scangle_it8.249
r_dihedral_angle_1_deg6.848
r_scbond_it5.833
r_mcangle_it4.388
r_mcbond_it2.536
r_angle_refined_deg2.223
r_chiral_restr0.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.59
r_dihedral_angle_4_deg21.238
r_dihedral_angle_3_deg18.394
r_scangle_it8.249
r_dihedral_angle_1_deg6.848
r_scbond_it5.833
r_mcangle_it4.388
r_mcbond_it2.536
r_angle_refined_deg2.223
r_chiral_restr0.118
r_bond_refined_d0.019
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_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 Atoms6469
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms707

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing