7PR4

Cocrystal Form II of a cytochrome c, sulfonato-thiacalix[4]arene - zinc cluster


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LYC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629320% PEG 3350, 100 mM sodium acetate pH 5.6, 10 mM zinc acetate
Crystal Properties
Matthews coefficientSolvent content
2.0540.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.624α = 90
b = 36.106β = 90
c = 82.898γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.98SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.341.4599.60.2170.0650.98413.310.626001
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.30.8810.4180.798

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 REPLACEMENTTHROUGHOUT5LYC1.3241.451.3525954130699.430.18870.18680.22516.2965
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms841
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms112

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing