4IN5

(M)L214G mutant of the Rhodobacter sphaeroides Reaction Center


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J8CPDB ENTRY 2J8C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42981 M potassium phosphate, 3.5% 1,2,3-heptanetriol, and 0.1% LDAO precipitant solution, 1.52 M potassium phosphate reservoir solution, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
5.4577.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.109α = 90
b = 139.109β = 90
c = 184.692γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2011-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11.0CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.2120.47299.90.08411.35.5105008105008
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.321000.590.591.25.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2J8C2.255.6257918899648523999.860.182490.181230.20619RANDOM44.899
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]
0.240.240.24-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.971
r_dihedral_angle_4_deg18.15
r_dihedral_angle_3_deg13.399
r_dihedral_angle_1_deg6.425
r_scangle_it3.519
r_angle_refined_deg2.633
r_scbond_it2.353
r_mcangle_it1.441
r_angle_other_deg1.105
r_mcbond_it0.802
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.971
r_dihedral_angle_4_deg18.15
r_dihedral_angle_3_deg13.399
r_dihedral_angle_1_deg6.425
r_scangle_it3.519
r_angle_refined_deg2.633
r_scbond_it2.353
r_mcangle_it1.441
r_angle_other_deg1.105
r_mcbond_it0.802
r_chiral_restr0.111
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6465
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms755

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XSCALEdata scaling