7MH9

Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant; Y(M210)3-nitrotyrosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J8CCHLROTYROSINE MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82931 M potassium phosphate, 3.5% 1,2,3-heptanetriol, and 0.1% LDAO precipitant solution; 1.4-1.5 M potassium phosphate reservoir solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
5.6878.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.21α = 90
b = 141.21β = 90
c = 187.59γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER X 16MRh coated collimating mirror, Toroidal focusing mirror2019-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL14-11.19499SSRLBL14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
13.139.0799.90.3470.3580.9947.1816.623979952.089
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.181001.5331.580.7061.6317.05

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTCHLROTYROSINE MODEL3.139.0737808199099.90.17110.16940.2052RANDOM58.559
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]
0.380.190.38-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.436
r_dihedral_angle_4_deg16.86
r_dihedral_angle_3_deg16.195
r_dihedral_angle_1_deg6.76
r_angle_refined_deg2.218
r_angle_other_deg1.173
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.436
r_dihedral_angle_4_deg16.86
r_dihedral_angle_3_deg16.195
r_dihedral_angle_1_deg6.76
r_angle_refined_deg2.218
r_angle_other_deg1.173
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5740
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms1355

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing