6Y0J

Cytochrome c in complex with phosphonato-calix[6]arene and sulfonato-calix[8]arene


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29310 % PEG 8000, 8 % ethylene glycol, 100 mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
5.1273

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.573α = 90
b = 67.573β = 90
c = 373.866γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2018-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.98008SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.762.311000.7040.1630.9395.3201620656.24
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.73.050.5920.097

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 REPLACEMENTTHROUGHOUT3TYI2.762.311616775461.50.2460.2450.269RANDOM60.16
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]
-5.2644-5.264410.5288
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion21.04
t_omega_torsion2.41
t_angle_deg1.13
t_bond_d0.009
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_trig_c_planes
t_utility_distance
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion21.04
t_omega_torsion2.41
t_angle_deg1.13
t_bond_d0.009
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_trig_c_planes
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
t_dihedral_angle_d
t_gen_planes
t_it
t_sum_occupancies
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3347
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms652

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction