7Q7F

Room temperature structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H mutant at atmospheric pressure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V3Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE28920-25 mg/ml protein solution was mixed 1:1 with lipid sponge phase. The mixture was filled into a sealed plastic tip covered with an excess amount of 1 M trisodium citrate and incubated in the dark at 289 K for 1 week.
Crystal Properties
Matthews coefficientSolvent content
3.4264

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.5α = 90
b = 102.5β = 90
c = 237.84γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295PIXELDECTRIS PILATUS3 X CdTe 2M2019-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P110.477PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.7547.0799.770.4140.4350.1280.9765.1310.73382649.57
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.84899.612.3512.4750.7510.3551.029.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3V3Y2.7547.071.3433811135899.810.18090.17910.224456.02
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.2154
f_angle_d0.5546
f_chiral_restr0.0389
f_plane_restr0.0036
f_bond_d0.0025
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6466
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms674

Software

Software
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing