2HJ6

Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated phosphatidylserine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUnpublished structure of reaction centre at 1.95A resolution

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8289Potassium phosphate, LDAO, 1,2,3-heptanetriol, 1,2,3-hexanetriol, dioxane, NaCl, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 16.0K
Crystal Properties
Matthews coefficientSolvent content
5.4777.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.355α = 90
b = 139.355β = 90
c = 183.217γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2005-05-20MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.10.92SRSPX10.1

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
1339.2999.70.08515.36.94153381.1
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)
133.161000.5753.176031

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTUnpublished structure of reaction centre at 1.95A resolution339.294149439411208399.430.176830.176830.174070.22719RANDOM57.076
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]
-0.33-0.17-0.330.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.813
r_dihedral_angle_3_deg17.15
r_dihedral_angle_4_deg16.249
r_dihedral_angle_1_deg6.5
r_scangle_it2.788
r_angle_refined_deg1.938
r_scbond_it1.799
r_angle_other_deg1.171
r_mcangle_it1.118
r_mcbond_it0.588
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.813
r_dihedral_angle_3_deg17.15
r_dihedral_angle_4_deg16.249
r_dihedral_angle_1_deg6.5
r_scangle_it2.788
r_angle_refined_deg1.938
r_scbond_it1.799
r_angle_other_deg1.171
r_mcangle_it1.118
r_mcbond_it0.588
Cruickshank estimated coordinate error0.502
r_symmetry_hbond_refined0.336
r_nbd_refined0.234
r_symmetry_vdw_other0.232
r_symmetry_vdw_refined0.222
r_nbtor_refined0.207
r_nbd_other0.205
Maximum Likelihood estimated coordinate error0.192
r_xyhbond_nbd_refined0.184
r_xyhbond_nbd_other0.129
r_mcbond_other0.108
r_metal_ion_refined0.098
r_chiral_restr0.093
r_nbtor_other0.093
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6476
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms787

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing