5NOQ

Structure of cyclophilin A in complex with 3-chloropyridin-2-amine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8279.15PEG 8000, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.7154.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.18α = 90
b = 53.88β = 90
c = 85.91γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.645.6599.90.147.95.426543
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6399.90.742.35.71327

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 REPLACEMENTTHROUGHOUT5LUD1.645.6525209127899.710.166740.165250.19617RANDOM19.348
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]
-0.030.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.132
r_dihedral_angle_4_deg18.822
r_dihedral_angle_3_deg11.877
r_dihedral_angle_1_deg6.915
r_long_range_B_refined6.234
r_long_range_B_other6.233
r_scangle_other4.668
r_scbond_it3.153
r_scbond_other3.153
r_mcangle_it2.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.132
r_dihedral_angle_4_deg18.822
r_dihedral_angle_3_deg11.877
r_dihedral_angle_1_deg6.915
r_long_range_B_refined6.234
r_long_range_B_other6.233
r_scangle_other4.668
r_scbond_it3.153
r_scbond_other3.153
r_mcangle_it2.8
r_mcangle_other2.799
r_angle_refined_deg1.975
r_mcbond_it1.951
r_mcbond_other1.95
r_angle_other_deg1.089
r_chiral_restr0.141
r_bond_refined_d0.023
r_gen_planes_refined0.013
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 Atoms159
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing