5A0E

Crystal structure of cyclophilin D in complex with CsA analogue, JW47.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2.9HANGING DROP 50:50. PRECIPITANT: 23% POLYETHYLENE GLYCOL (PEG3350), 50 MM SODIUM-CITRATE BUFFER AT PH 2.9 PROTEIN: 30 MG/ML IN 50MM POTASSIUM/SODIUM PHOSPHATE PH 7.3, 100MM NACL, 2MM EDTA, 0.02% SODIUM AZIDE.
Crystal Properties
Matthews coefficientSolvent content
2.0439.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.12α = 90
b = 69.51β = 90
c = 109.17γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2015-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.1235.9990.50.0620.411.8101898
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)
11.121.1545.81.041.86.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2Z6W1.2535.9975156396497.480.099710.098060.13122RANDOM15.02
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free30.806
r_dihedral_angle_2_deg28.953
r_dihedral_angle_4_deg17.751
r_dihedral_angle_3_deg11.976
r_sphericity_bonded11.736
r_dihedral_angle_1_deg6.765
r_rigid_bond_restr6.193
r_scbond_it4.204
r_mcangle_it3.3
r_angle_other_deg3.101
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free30.806
r_dihedral_angle_2_deg28.953
r_dihedral_angle_4_deg17.751
r_dihedral_angle_3_deg11.976
r_sphericity_bonded11.736
r_dihedral_angle_1_deg6.765
r_rigid_bond_restr6.193
r_scbond_it4.204
r_mcangle_it3.3
r_angle_other_deg3.101
r_mcbond_it2.678
r_mcbond_other2.677
r_angle_refined_deg2.137
r_chiral_restr0.3
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_gen_planes_other0.004
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2680
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing