6GJJ

Cyclophilin A complexed with tri-vector ligand 2.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8279.15PEG 8000, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.8657.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.99α = 90
b = 53.88β = 90
c = 89.15γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.3846.1199.80.0450.999166.343264
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)
11.383.7499.80.6650.6321.36.4

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 REPLACEMENTTHROUGHOUT5NOY1.3846.1141063209999.550.153660.152010.18514RANDOM27.445
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]
1.43-0.87-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.283
r_dihedral_angle_2_deg32.926
r_dihedral_angle_4_deg18.966
r_dihedral_angle_3_deg12.759
r_sphericity_bonded12.619
r_dihedral_angle_1_deg5.795
r_long_range_B_refined5.267
r_long_range_B_other5.265
r_scangle_other3.145
r_rigid_bond_restr2.861
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.283
r_dihedral_angle_2_deg32.926
r_dihedral_angle_4_deg18.966
r_dihedral_angle_3_deg12.759
r_sphericity_bonded12.619
r_dihedral_angle_1_deg5.795
r_long_range_B_refined5.267
r_long_range_B_other5.265
r_scangle_other3.145
r_rigid_bond_restr2.861
r_scbond_it2.802
r_scbond_other2.8
r_mcangle_other2.564
r_mcangle_it2.564
r_mcbond_it2.143
r_mcbond_other2.142
r_angle_refined_deg1.65
r_angle_other_deg1.025
r_chiral_restr0.114
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_refined
r_symmetry_metal_ion_other
r_symmetry_vdw_other
r_metal_ion_other
r_metal_ion_refined
r_xyhbond_nbd_other
r_symmetry_hbond_refined
r_nbtor_other
r_scangle_it
r_nbtor_refined
r_nbd_other
r_nbd_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1266
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing