6GJP

Cyclophilin A complexed with tri-vector ligand 7.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8279.15PEG 8000, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.8256.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.496α = 90
b = 54.286β = 90
c = 88.182γ = 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)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
11.93954.28699.60.1590.992115.715641
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9391.97399.70.6874

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 REPLACEMENTTHROUGHOUT5NOY1.9446.231479981299.360.17810.174950.23726RANDOM29.249
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]
-0.050.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.853
r_dihedral_angle_4_deg16.838
r_dihedral_angle_3_deg12.814
r_dihedral_angle_1_deg7.106
r_long_range_B_refined6.997
r_long_range_B_other6.995
r_scangle_other4.634
r_mcangle_other3.476
r_mcangle_it3.472
r_scbond_it3.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.853
r_dihedral_angle_4_deg16.838
r_dihedral_angle_3_deg12.814
r_dihedral_angle_1_deg7.106
r_long_range_B_refined6.997
r_long_range_B_other6.995
r_scangle_other4.634
r_mcangle_other3.476
r_mcangle_it3.472
r_scbond_it3.03
r_scbond_other3.028
r_mcbond_it2.427
r_mcbond_other2.397
r_angle_refined_deg1.755
r_angle_other_deg1.103
r_chiral_restr0.099
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms182
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing