2HG9 | pdb_00002hg9

Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with tetrabrominated phosphatidylcholine


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, dioxane, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 16.0K
Crystal Properties
Matthews coefficientSolvent content
5.5277.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.554α = 90
b = 139.554β = 90
c = 184.609γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2004-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.87SRSPX9.6

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
12.4539.3799.70.068188.67658851.5
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)
12.452.581000.6143.87.811112

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTUnpublished structure of reaction centre at 1.95A resolution2.4539.367522771518370997.960.180350.180350.17880.180.209140.21RANDOM44.677
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]
0.860.430.86-1.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.208
r_dihedral_angle_4_deg18.081
r_dihedral_angle_3_deg14.632
r_dihedral_angle_1_deg5.892
r_scangle_it3.307
r_scbond_it2.33
r_angle_refined_deg1.738
r_mcangle_it1.353
r_angle_other_deg1.244
r_mcbond_it0.751
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.208
r_dihedral_angle_4_deg18.081
r_dihedral_angle_3_deg14.632
r_dihedral_angle_1_deg5.892
r_scangle_it3.307
r_scbond_it2.33
r_angle_refined_deg1.738
r_mcangle_it1.353
r_angle_other_deg1.244
r_mcbond_it0.751
r_symmetry_vdw_other0.289
r_nbd_refined0.221
r_nbd_other0.201
r_symmetry_hbond_refined0.201
Cruickshank estimated coordinate error0.198
r_nbtor_refined0.196
r_mcbond_other0.195
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.162
Maximum Likelihood estimated coordinate error0.115
r_metal_ion_refined0.108
r_chiral_restr0.105
r_nbtor_other0.092
r_xyhbond_nbd_other0.039
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6475
Nucleic Acid Atoms
Solvent Atoms441
Heterogen Atoms853

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing