6GD6

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2931.75 M ammonium sulfate 0.2 M NaCl (2x protein solution : 1x crystallisation condition)

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.003α = 90
b = 82.003β = 90
c = 82.535γ = 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)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
11.235.6899.80.0550.0640.0320.9989.93.764600
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)
11.21.2299.50.5330.6360.3410.7353.3

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 A1.235.6861332323899.760.11970.11890.1361RANDOM18.231
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]
0.080.040.08-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.406
r_sphericity_free24.714
r_dihedral_angle_4_deg17.414
r_dihedral_angle_3_deg11.771
r_sphericity_bonded8.366
r_dihedral_angle_1_deg6.461
r_angle_refined_deg1.48
r_rigid_bond_restr0.961
r_angle_other_deg0.873
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.406
r_sphericity_free24.714
r_dihedral_angle_4_deg17.414
r_dihedral_angle_3_deg11.771
r_sphericity_bonded8.366
r_dihedral_angle_1_deg6.461
r_angle_refined_deg1.48
r_rigid_bond_restr0.961
r_angle_other_deg0.873
r_chiral_restr0.096
r_gen_planes_refined0.013
r_gen_planes_other0.013
r_bond_refined_d0.011
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms846
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms164

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction