6GJN

Cyclophilin A complexed with tri-vector ligand 15.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP279.15PEG 8000, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.7655.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.952α = 90
b = 53.348β = 90
c = 88.898γ = 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 I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.745.7599.60.1860.2060.0868.3922682
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.731000.60.6780.31213

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 REPLACEMENTTHROUGHOUT5NOY1.745.7421393115599.060.171220.169540.2029RANDOM17.689
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]
0.010.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.182
r_dihedral_angle_4_deg16.342
r_dihedral_angle_3_deg12.213
r_dihedral_angle_1_deg6.594
r_long_range_B_refined5.675
r_long_range_B_other5.674
r_scangle_other3.114
r_mcangle_other2.709
r_mcangle_it2.695
r_angle_refined_deg2.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.182
r_dihedral_angle_4_deg16.342
r_dihedral_angle_3_deg12.213
r_dihedral_angle_1_deg6.594
r_long_range_B_refined5.675
r_long_range_B_other5.674
r_scangle_other3.114
r_mcangle_other2.709
r_mcangle_it2.695
r_angle_refined_deg2.107
r_scbond_it2.048
r_scbond_other2.031
r_mcbond_it1.682
r_mcbond_other1.681
r_angle_other_deg1.182
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1266
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing