7MH5

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


X-RAY DIFFRACTION

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
5.6678.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.414α = 90
b = 141.414β = 90
c = 186.502γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray250PIXELDECTRIS PILATUS 6M2017-08-11MSINGLE 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
12.8538.9599.90.1160.1260.99812.186.7115080772.806
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)
12.852.921001.2871.3910.5821.616.964

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 Photosynthetic Reaction Center variant with Chlorotyrosine at M2102.8538.9548339249599.880.18140.18020.205RANDOM68.929
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]
0.10.050.1-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.152
r_dihedral_angle_4_deg17.832
r_dihedral_angle_3_deg16.208
r_dihedral_angle_1_deg7.097
r_angle_refined_deg2.209
r_angle_other_deg1.148
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.152
r_dihedral_angle_4_deg17.832
r_dihedral_angle_3_deg16.208
r_dihedral_angle_1_deg7.097
r_angle_refined_deg2.209
r_angle_other_deg1.148
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6451
Nucleic Acid Atoms
Solvent Atoms184
Heterogen Atoms617

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing