6GJR

Cyclophilin A complexed with tri-vector ligand 9.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8279.15PEG 8000, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.7555.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.51α = 90
b = 53.17β = 90
c = 87.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97947DiamondI04

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
11.6538.396.380.1240.1370.0580.99374.723700
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)
11.651.6890.80.4820.5621.23.6

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 REPLACEMENTTHROUGHOUT5NOY1.6938.321583117599.180.203160.200020.26183RANDOM32.032
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]
0.15-0.08-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.152
r_dihedral_angle_4_deg23.103
r_dihedral_angle_3_deg14.877
r_long_range_B_refined7.784
r_long_range_B_other7.782
r_dihedral_angle_1_deg6.926
r_scangle_other5.075
r_mcangle_other4.279
r_mcangle_it4.238
r_scbond_it3.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.152
r_dihedral_angle_4_deg23.103
r_dihedral_angle_3_deg14.877
r_long_range_B_refined7.784
r_long_range_B_other7.782
r_dihedral_angle_1_deg6.926
r_scangle_other5.075
r_mcangle_other4.279
r_mcangle_it4.238
r_scbond_it3.308
r_scbond_other3.305
r_mcbond_it2.836
r_mcbond_other2.834
r_angle_refined_deg1.95
r_angle_other_deg1.032
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms161
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing