6GDA

Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form soaked with Spermine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YCC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2932.1 M ammonium sulfate 0.1 M MES pH 6.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.252α = 90
b = 101.252β = 90
c = 85.31γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2017-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.980SOLEILPROXIMA 2

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
12.885.311000.1230.1310.0450.99712.18.211454
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)
12.82.951000.6660.710.2430.4738.5

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 REPLACEMENTTHROUGHOUT1YCC2.871.7108445701000.2230.22190.243RANDOM68.516
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]
-1.47-1.472.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.912
r_dihedral_angle_3_deg13.424
r_dihedral_angle_4_deg10.923
r_dihedral_angle_1_deg5.189
r_angle_refined_deg1.192
r_angle_other_deg0.714
r_chiral_restr0.065
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.912
r_dihedral_angle_3_deg13.424
r_dihedral_angle_4_deg10.923
r_dihedral_angle_1_deg5.189
r_angle_refined_deg1.192
r_angle_other_deg0.714
r_chiral_restr0.065
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms846
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms404

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction