4ZSD

Human Cyclophilin D Complexed with an Inhibitor at room temperature


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.329130% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.1141.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.943α = 90
b = 57.943β = 90
c = 88.57γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 315r2015-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9797ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4557.9499.27225914

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.4548.4925914133599.180.13490.13380.1554RANDOM12.549
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]
0.140.14-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.051
r_sphericity_free20.119
r_dihedral_angle_4_deg13.913
r_dihedral_angle_3_deg10.917
r_dihedral_angle_1_deg5.836
r_rigid_bond_restr5.65
r_sphericity_bonded3.302
r_angle_other_deg1.305
r_angle_refined_deg1.303
r_mcangle_it0.891
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.051
r_sphericity_free20.119
r_dihedral_angle_4_deg13.913
r_dihedral_angle_3_deg10.917
r_dihedral_angle_1_deg5.836
r_rigid_bond_restr5.65
r_sphericity_bonded3.302
r_angle_other_deg1.305
r_angle_refined_deg1.303
r_mcangle_it0.891
r_mcbond_it0.707
r_mcbond_other0.706
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1223
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms32

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
Cootmodel building