☰ Navigation Tabs
Cyclophilin A single mutant D66A in complex with an inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RDD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 2.2 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 3.01 59.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.01 α = 90 b = 63.01 β = 90 c = 94.72 γ = 120
Symmetry Space Group P 32 2 1
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 DECTRIS PILATUS 2M 2017-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.16 47.28 99.64 0.048 0.017 0.999 14.2 9.1 75550
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.16 1.18 99.27 0.723 0.704 1 6.5
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 3RDD 1.16 47.28 71625 3921 99.64 0.15075 0.1497 0.1546 0.1699 0.1761 RANDOM 27.891
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] 0.51 0.26 0.51 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.825 r_sphericity_free 31.419 r_dihedral_angle_4_deg 21.193 r_sphericity_bonded 16.537 r_dihedral_angle_3_deg 12.168 r_dihedral_angle_1_deg 6.044 r_long_range_B_refined 4.492 r_long_range_B_other 4.491 r_mcangle_other 4.198 r_mcangle_it 4.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.825 r_sphericity_free 31.419 r_dihedral_angle_4_deg 21.193 r_sphericity_bonded 16.537 r_dihedral_angle_3_deg 12.168 r_dihedral_angle_1_deg 6.044 r_long_range_B_refined 4.492 r_long_range_B_other 4.491 r_mcangle_other 4.198 r_mcangle_it 4.197 r_mcbond_it 3.091 r_mcbond_other 3.088 r_scangle_other 2.44 r_scbond_it 2.08 r_scbond_other 2.079 r_angle_refined_deg 1.373 r_rigid_bond_restr 1.194 r_angle_other_deg 0.92 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1222 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement xia2 data reduction pointless data scaling REFMAC phasing