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Cyclophilin A complexed with tri-vector ligand 2.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 279.15 PEG 8000, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.86 57.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.99 α = 90 b = 53.88 β = 90 c = 89.15 γ = 90
Symmetry Space Group P 21 21 21
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 6M-F 2017-05-14 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) 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 1.38 46.11 99.8 0.045 0.999 16 6.3 43264
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 1.38 3.74 99.8 0.665 0.632 1.3 6.4
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 5NOY 1.38 46.11 41063 2099 99.55 0.15366 0.15201 0.1526 0.18514 0.1879 RANDOM 27.445
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] 1.43 -0.87 -0.57
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.283 r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 18.966 r_dihedral_angle_3_deg 12.759 r_sphericity_bonded 12.619 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 5.267 r_long_range_B_other 5.265 r_scangle_other 3.145 r_rigid_bond_restr 2.861
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.283 r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 18.966 r_dihedral_angle_3_deg 12.759 r_sphericity_bonded 12.619 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 5.267 r_long_range_B_other 5.265 r_scangle_other 3.145 r_rigid_bond_restr 2.861 r_scbond_it 2.802 r_scbond_other 2.8 r_mcangle_it 2.564 r_mcangle_other 2.564 r_mcbond_it 2.143 r_mcbond_other 2.142 r_angle_refined_deg 1.65 r_angle_other_deg 1.025 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1266 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing