6GJI

Cyclophilin A complexed with the tri-vector ligand 8.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8279.15PEG 8000, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.8256.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.621α = 90
b = 54.535β = 90
c = 87.486γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979500DiamondI04

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
11.59787.48699.90.070.080.0430.99813.56.327755
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)
11.5971.6251000.6210.6890.3660.8862.46.6

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 REPLACEMENTTHROUGHOUT5NOY1.646.2826324143199.920.154490.152540.19071RANDOM29.126
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]
0.05-0.01-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.14
r_dihedral_angle_4_deg18.812
r_dihedral_angle_3_deg12.206
r_long_range_B_refined9.364
r_long_range_B_other9.351
r_dihedral_angle_1_deg6.22
r_scangle_other6.07
r_mcangle_other3.998
r_mcangle_it3.949
r_scbond_it3.873
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.14
r_dihedral_angle_4_deg18.812
r_dihedral_angle_3_deg12.206
r_long_range_B_refined9.364
r_long_range_B_other9.351
r_dihedral_angle_1_deg6.22
r_scangle_other6.07
r_mcangle_other3.998
r_mcangle_it3.949
r_scbond_it3.873
r_scbond_other3.866
r_mcbond_it2.582
r_mcbond_other2.479
r_angle_refined_deg1.996
r_angle_other_deg1.26
r_chiral_restr0.144
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.002
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1266
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing