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Crystal structure at room temperature of cyclophilin D in complex with an inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 298 25% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.11 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58 α = 90 b = 58 β = 90 c = 88.41 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 210 2014-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.542
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 2.23 29.5 98.1 18.8 4.5 6820
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.23 29.02 6820 330 91.78 0.1421 0.14 0.2361 0.1863 1.792 RANDOM 17.087
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] 0.06 0.06 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.982 r_dihedral_angle_4_deg 19.501 r_dihedral_angle_3_deg 13.439 r_dihedral_angle_1_deg 6.036 r_angle_refined_deg 1.321 r_mcangle_it 1.28 r_mcbond_it 0.762 r_mcbond_other 0.761 r_angle_other_deg 0.743 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.982 r_dihedral_angle_4_deg 19.501 r_dihedral_angle_3_deg 13.439 r_dihedral_angle_1_deg 6.036 r_angle_refined_deg 1.321 r_mcangle_it 1.28 r_mcbond_it 0.762 r_mcbond_other 0.761 r_angle_other_deg 0.743 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1230 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 18
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing