6GD7

Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with PEG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LYC5LYC chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2935 % PEG 3350 (2x protein solution : 1x crystallisation condition)

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.42α = 90
b = 81.42β = 90
c = 82.364γ = 120
Symmetry
Space GroupH 3

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)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
11.5540.7199.90.0560.026112.84.429520
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)
11.551.5899.90.5160.2560.493.9

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 REPLACEMENTTHROUGHOUT5LYC chain A1.5540.7128013150199.880.1510.14930.1835RANDOM30.532
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]
0.560.280.56-1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.404
r_dihedral_angle_4_deg24.262
r_dihedral_angle_3_deg12.815
r_sphericity_bonded7.767
r_dihedral_angle_1_deg5.673
r_rigid_bond_restr1.604
r_angle_refined_deg1.437
r_angle_other_deg0.973
r_chiral_restr0.088
r_bond_refined_d0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.404
r_dihedral_angle_4_deg24.262
r_dihedral_angle_3_deg12.815
r_sphericity_bonded7.767
r_dihedral_angle_1_deg5.673
r_rigid_bond_restr1.604
r_angle_refined_deg1.437
r_angle_other_deg0.973
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms846
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms145

Software

Software
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction