6GJY

Cyclophilin A complexed with tri-vector ligand 5.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP279.15PEG 8000, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.7455.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.59α = 90
b = 52.84β = 90
c = 87.98γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.90001DiamondI04

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
11.2945.398.890.0620.0680.0270.99912.1650202
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)
11.291.3198.750.6020.5051.2

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 REPLACEMENTTHROUGHOUT5NOY1.2945.347575253398.690.164880.163710.18791RANDOM21.798
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.79
r_dihedral_angle_4_deg22.347
r_dihedral_angle_3_deg12.02
r_long_range_B_refined7.704
r_long_range_B_other7.701
r_dihedral_angle_1_deg5.859
r_scangle_other4.463
r_mcangle_other3.053
r_mcangle_it3.029
r_scbond_it2.852
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.79
r_dihedral_angle_4_deg22.347
r_dihedral_angle_3_deg12.02
r_long_range_B_refined7.704
r_long_range_B_other7.701
r_dihedral_angle_1_deg5.859
r_scangle_other4.463
r_mcangle_other3.053
r_mcangle_it3.029
r_scbond_it2.852
r_scbond_other2.851
r_angle_refined_deg2.11
r_mcbond_it1.99
r_mcbond_other1.989
r_angle_other_deg1.069
r_chiral_restr0.138
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 Atoms300
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing