X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629320 % PEG 8000, 50 mM NaCl, 50 mM sodium acetate (pH 5.6). [Cytochrome c] = 0.75 mM and [Methylphosphonatocalix[4]arene] = 0.3 mM
Crystal Properties
Matthews coefficientSolvent content
2.3948.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.917α = 90
b = 80.227β = 93.07
c = 47.807γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.979APS24-ID-C

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
11.547.7499.20.0550.0260.99918.75.534591
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5599.40.0550.1585.15.4

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 REPLACEMENTTHROUGHOUT1YCC1.547.7432897170799.230.17190.17040.2012RANDOM20.624
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]
0.3-2.11-0.880.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.978
r_dihedral_angle_4_deg24.671
r_dihedral_angle_3_deg14.117
r_dihedral_angle_1_deg6.26
r_angle_refined_deg1.608
r_angle_other_deg1.012
r_chiral_restr0.122
r_gen_planes_refined0.012
r_bond_refined_d0.011
r_gen_planes_other0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.978
r_dihedral_angle_4_deg24.671
r_dihedral_angle_3_deg14.117
r_dihedral_angle_1_deg6.26
r_angle_refined_deg1.608
r_angle_other_deg1.012
r_chiral_restr0.122
r_gen_planes_refined0.012
r_bond_refined_d0.011
r_gen_planes_other0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1624
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms295

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing