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Human Cyclophilin D Complexed with Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BIT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 294 4M potassium formate, 0.1M BIS-TRIS propane, 2% w/v PEG2000mme
Crystal Properties Matthews coefficient Solvent content 2.67 53.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.45 α = 90 b = 57.45 β = 90 c = 114.05 γ = 90
Symmetry Space Group P 43 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 100 PIXEL PSI PILATUS 6M 2013-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.984 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.8 38.2 96.5 0.101 0.056 11 4.6 17696 81366
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 91.9 0.121 7.5 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2bit 1.8 38.2 16745 904 95.82 0.18041 0.17896 0.1893 0.20749 0.2122 RANDOM 17.658
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.427 r_dihedral_angle_4_deg 15.542 r_dihedral_angle_3_deg 12.716 r_dihedral_angle_1_deg 6.759 r_long_range_B_other 5.908 r_long_range_B_refined 5.907 r_scangle_other 3.851 r_scbond_it 2.523 r_scbond_other 2.521 r_angle_refined_deg 2.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.427 r_dihedral_angle_4_deg 15.542 r_dihedral_angle_3_deg 12.716 r_dihedral_angle_1_deg 6.759 r_long_range_B_other 5.908 r_long_range_B_refined 5.907 r_scangle_other 3.851 r_scbond_it 2.523 r_scbond_other 2.521 r_angle_refined_deg 2.006 r_mcangle_it 1.905 r_mcangle_other 1.904 r_mcbond_it 1.389 r_mcbond_other 1.388 r_angle_other_deg 1.108 r_chiral_restr 0.124 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1240 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing