2Z6W

Crystal structure of human cyclophilin D in complex with cyclosporin A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BIT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12.920% PEG 3350, PH 2.9, VAPOR DIFFUSION, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.0138.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.882α = 90
b = 69.313β = 90
c = 112.077γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XUSPring-8BL41XU

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
10.9620097.70.05918.62.8180558-3
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)
10.960.9796.60.4142.4

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 REPLACEMENTTHROUGHOUT2BIT0.9656.08171367913197.60.130.1290.153RANDOM8.23
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]
0.4-0.470.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.258
r_dihedral_angle_4_deg16.427
r_dihedral_angle_3_deg12.557
r_sphericity_free9.446
r_dihedral_angle_1_deg6.576
r_sphericity_bonded5.116
r_scangle_it3.776
r_scbond_it2.853
r_mcangle_it2.339
r_angle_refined_deg1.826
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.258
r_dihedral_angle_4_deg16.427
r_dihedral_angle_3_deg12.557
r_sphericity_free9.446
r_dihedral_angle_1_deg6.576
r_sphericity_bonded5.116
r_scangle_it3.776
r_scbond_it2.853
r_mcangle_it2.339
r_angle_refined_deg1.826
r_mcbond_it1.732
r_rigid_bond_restr1.54
r_nbtor_refined0.323
r_nbd_refined0.251
r_symmetry_vdw_refined0.233
r_symmetry_hbond_refined0.133
r_xyhbond_nbd_refined0.126
r_chiral_restr0.111
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2650
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms13

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling