2HG3 | pdb_00002hg3

Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with brominated 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
5.5477.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.844α = 90
b = 139.844β = 90
c = 184.335γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2004-01-17MSINGLE 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
12.734.3699.90.08214.65.85784057.8
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)
12.72.851000.6292.65.88353

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 resolution2.734.355752954677285299.660.166240.166240.164440.170.199440.2RANDOM42.887
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]
0.30.150.3-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.671
r_dihedral_angle_4_deg18.382
r_dihedral_angle_3_deg15.748
r_dihedral_angle_1_deg6.175
r_scangle_it3.274
r_scbond_it2.205
r_angle_refined_deg1.856
r_mcangle_it1.253
r_angle_other_deg1.25
r_mcbond_it0.674
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.671
r_dihedral_angle_4_deg18.382
r_dihedral_angle_3_deg15.748
r_dihedral_angle_1_deg6.175
r_scangle_it3.274
r_scbond_it2.205
r_angle_refined_deg1.856
r_mcangle_it1.253
r_angle_other_deg1.25
r_mcbond_it0.674
r_symmetry_vdw_other0.265
r_nbd_refined0.226
r_symmetry_vdw_refined0.224
r_symmetry_hbond_refined0.218
r_nbd_other0.202
r_nbtor_refined0.2
r_xyhbond_nbd_refined0.161
r_mcbond_other0.148
r_chiral_restr0.098
r_nbtor_other0.093
r_metal_ion_refined0.045
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6468
Nucleic Acid Atoms
Solvent Atoms452
Heterogen Atoms895

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing