5NOY

Structure of cyclophilin A in complex with 3,4-diaminobenzamide


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
2.8356.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.87α = 90
b = 54.58β = 90
c = 87.44γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.920DiamondI04-1

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
11.4338.4999.20.0618.86.838376
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)
11.431.4795.30.612.76.1

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 REPLACEMENTTHROUGHOUT5LUD1.4338.4936396192199.10.158660.157430.18247RANDOM18.09
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]
0.29-0.25-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.433
r_dihedral_angle_4_deg17.766
r_dihedral_angle_3_deg11.528
r_dihedral_angle_1_deg6.167
r_long_range_B_refined6.076
r_long_range_B_other6.075
r_scangle_other3.591
r_mcangle_other2.495
r_mcangle_it2.493
r_scbond_it2.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.433
r_dihedral_angle_4_deg17.766
r_dihedral_angle_3_deg11.528
r_dihedral_angle_1_deg6.167
r_long_range_B_refined6.076
r_long_range_B_other6.075
r_scangle_other3.591
r_mcangle_other2.495
r_mcangle_it2.493
r_scbond_it2.236
r_scbond_other2.235
r_angle_refined_deg1.742
r_mcbond_other1.575
r_mcbond_it1.574
r_angle_other_deg1.024
r_chiral_restr0.11
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.008
r_bond_other_d0.002
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 Atoms244
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing