6GJM

Cyclophilin A complexed with tri-vector ligand 4.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NOY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8279.15PEG 8000, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.8156.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.726α = 90
b = 54.378β = 90
c = 87.283γ = 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 I040.97950DiamondI04

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
11.35487.28399.90.0730.99911.66.245033
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.3541.3771000.4890.912.26.3

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 REPLACEMENTTHROUGHOUT5NOY1.35434.0442741227499.870.161640.160760.17784RANDOM20.723
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]
0.02-0.560.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.473
r_dihedral_angle_4_deg16.545
r_dihedral_angle_3_deg11.007
r_dihedral_angle_1_deg5.7
r_long_range_B_refined4.567
r_long_range_B_other4.199
r_scangle_other1.973
r_mcangle_other1.675
r_mcangle_it1.673
r_angle_refined_deg1.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.473
r_dihedral_angle_4_deg16.545
r_dihedral_angle_3_deg11.007
r_dihedral_angle_1_deg5.7
r_long_range_B_refined4.567
r_long_range_B_other4.199
r_scangle_other1.973
r_mcangle_other1.675
r_mcangle_it1.673
r_angle_refined_deg1.297
r_scbond_it1.203
r_scbond_other1.186
r_mcbond_it1.001
r_mcbond_other0.992
r_angle_other_deg0.886
r_chiral_restr0.078
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms253
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing