2HHK | pdb_00002hhk

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


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
5.4977.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.417α = 90
b = 139.417β = 90
c = 183.701γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2005-03-18MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9192ESRFBM14

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
12.546.0399.60.05922.810.97148559.6
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)
12.52.6499.40.5434.61110292

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 resolution2.5467146967921354899.480.173470.173470.172230.180.196770.2RANDOM52.449
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]
-0.71-0.35-0.711.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.518
r_dihedral_angle_4_deg18.137
r_dihedral_angle_3_deg14.347
r_dihedral_angle_1_deg5.86
r_scangle_it3.24
r_scbond_it2.293
r_angle_refined_deg1.762
r_angle_other_deg1.541
r_mcangle_it1.324
r_mcbond_it0.728
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.518
r_dihedral_angle_4_deg18.137
r_dihedral_angle_3_deg14.347
r_dihedral_angle_1_deg5.86
r_scangle_it3.24
r_scbond_it2.293
r_angle_refined_deg1.762
r_angle_other_deg1.541
r_mcangle_it1.324
r_mcbond_it0.728
r_symmetry_vdw_other0.271
r_symmetry_hbond_refined0.27
r_nbd_refined0.221
Cruickshank estimated coordinate error0.203
r_nbd_other0.201
r_nbtor_refined0.197
r_mcbond_other0.181
r_xyhbond_nbd_refined0.178
r_symmetry_vdw_refined0.157
r_chiral_restr0.108
Maximum Likelihood estimated coordinate error0.104
r_nbtor_other0.093
r_metal_ion_refined0.086
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_xyhbond_nbd_other0.003
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 Atoms410
Heterogen Atoms818

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing