3I4D

Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82921M Potassium Phosphate, 90mM Sodium Chloride, 3% w/v Heptanetriol, 2% w/v Hexanetriol, 3% w/v Dioxane, 0.05% w/v LDAO, 10mM TRIS-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292.0K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.8α = 90
b = 138.8β = 90
c = 184.569γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMirrors2006-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW14A0.954Photon FactoryAR-NW14A

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
12.0130.25495.60.05821.37.313089713089733.61
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)
2.012.0867.10.5021.72.99061

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.0130.25117829117829613490.930.182530.181240.181240.20658RANDOM42.99
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]
0.350.180.35-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.91
r_dihedral_angle_4_deg18.895
r_dihedral_angle_3_deg13.383
r_dihedral_angle_1_deg5.479
r_scangle_it3.531
r_scbond_it2.58
r_angle_refined_deg1.922
r_mcangle_it1.626
r_angle_other_deg1.037
r_mcbond_it0.976
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.91
r_dihedral_angle_4_deg18.895
r_dihedral_angle_3_deg13.383
r_dihedral_angle_1_deg5.479
r_scangle_it3.531
r_scbond_it2.58
r_angle_refined_deg1.922
r_mcangle_it1.626
r_angle_other_deg1.037
r_mcbond_it0.976
r_mcbond_other0.305
r_symmetry_vdw_other0.273
r_nbd_refined0.226
r_symmetry_vdw_refined0.21
r_nbtor_refined0.203
r_nbd_other0.199
r_xyhbond_nbd_refined0.184
r_symmetry_hbond_refined0.171
r_chiral_restr0.122
r_nbtor_other0.092
r_metal_ion_refined0.066
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_symmetry_metal_ion_refined0.01
r_bond_other_d0.004
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6464
Nucleic Acid Atoms
Solvent Atoms553
Heterogen Atoms1228

Software

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