7MH4

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherModel from the Chloro derivative

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 Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.337α = 90
b = 141.337β = 90
c = 186.87γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray250PIXELDECTRIS PILATUS 6MRh coated collimating mirror, K-B focusing mirrors2017-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

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
12.483999.60.1080.1210.99610.165.0767655158.55
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)
12.482.5499.81.0281.1540.5881.694.855

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 REPLACEMENTTHROUGHOUTModel from the Chloro derivative2.483972899376899.70.16880.16760.1926RANDOM48.26
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]
0.080.040.08-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.5
r_dihedral_angle_4_deg17.547
r_dihedral_angle_3_deg14.706
r_dihedral_angle_1_deg6.533
r_angle_refined_deg2.219
r_angle_other_deg1.218
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.5
r_dihedral_angle_4_deg17.547
r_dihedral_angle_3_deg14.706
r_dihedral_angle_1_deg6.533
r_angle_refined_deg2.219
r_angle_other_deg1.218
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6442
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms628

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing