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Human Cyclophilin D Complexed with an Inhibitor at room temperature
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 291 30% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.1 41.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.866 α = 90 b = 57.866 β = 90 c = 88.463 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 315r 2015-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9797 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.5 48.4 73.1 12.1 2.8 16982
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.5 48.43 16982 862 72.05 0.135 0.1336 0.1628 0.1614 RANDOM 9.817
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.012 r_dihedral_angle_4_deg 17.501 r_sphericity_free 14.002 r_dihedral_angle_3_deg 12.404 r_dihedral_angle_1_deg 5.938 r_sphericity_bonded 2.256 r_angle_refined_deg 1.3 r_angle_other_deg 0.887 r_rigid_bond_restr 0.833 r_mcangle_it 0.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.012 r_dihedral_angle_4_deg 17.501 r_sphericity_free 14.002 r_dihedral_angle_3_deg 12.404 r_dihedral_angle_1_deg 5.938 r_sphericity_bonded 2.256 r_angle_refined_deg 1.3 r_angle_other_deg 0.887 r_rigid_bond_restr 0.833 r_mcangle_it 0.615 r_mcbond_it 0.495 r_mcbond_other 0.495 r_chiral_restr 0.082 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1225 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XSCALE data scaling Coot model building XDS data reduction REFMAC phasing