2HIT

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


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
5.4877.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.289α = 90
b = 139.289β = 90
c = 183.839γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 225 mm CCDmirrors2005-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.91929ESRFBM14

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
12.7546.0399.90.0662310.95410274.5
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)
12.752.91000.5694.311.17805

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 resolution2.7546.015409451405268999.960.183690.183690.18170.22193RANDOM60.047
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]
-0.2-0.1-0.20.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.48
r_dihedral_angle_4_deg20.88
r_dihedral_angle_3_deg16.568
r_dihedral_angle_1_deg6.335
r_scangle_it3.166
r_scbond_it2.127
r_angle_refined_deg1.878
r_angle_other_deg1.274
r_mcangle_it1.23
r_mcbond_it0.676
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.48
r_dihedral_angle_4_deg20.88
r_dihedral_angle_3_deg16.568
r_dihedral_angle_1_deg6.335
r_scangle_it3.166
r_scbond_it2.127
r_angle_refined_deg1.878
r_angle_other_deg1.274
r_mcangle_it1.23
r_mcbond_it0.676
r_symmetry_hbond_refined0.372
Cruickshank estimated coordinate error0.319
r_symmetry_vdw_other0.303
r_nbd_refined0.232
r_nbd_other0.203
r_nbtor_refined0.203
r_xyhbond_nbd_refined0.182
Maximum Likelihood estimated coordinate error0.152
r_symmetry_vdw_refined0.144
r_mcbond_other0.144
r_metal_ion_refined0.135
r_chiral_restr0.106
r_nbtor_other0.093
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 Atoms6494
Nucleic Acid Atoms
Solvent Atoms394
Heterogen Atoms799

Software

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