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Cyclophilin A complexed with tri-vector ligand 15.
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 279.15 PEG 8000, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.76 55.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.952 α = 90 b = 53.348 β = 90 c = 88.898 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 2017-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.7 45.75 99.6 0.186 0.206 0.086 8.3 9 22682
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 100 0.6 0.678 0.312 13
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 1.7 45.74 21393 1155 99.06 0.17122 0.16954 0.1807 0.2029 0.2111 RANDOM 17.689
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 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.182 r_dihedral_angle_4_deg 16.342 r_dihedral_angle_3_deg 12.213 r_dihedral_angle_1_deg 6.594 r_long_range_B_refined 5.675 r_long_range_B_other 5.674 r_scangle_other 3.114 r_mcangle_other 2.709 r_mcangle_it 2.695 r_angle_refined_deg 2.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.182 r_dihedral_angle_4_deg 16.342 r_dihedral_angle_3_deg 12.213 r_dihedral_angle_1_deg 6.594 r_long_range_B_refined 5.675 r_long_range_B_other 5.674 r_scangle_other 3.114 r_mcangle_other 2.709 r_mcangle_it 2.695 r_angle_refined_deg 2.107 r_scbond_it 2.048 r_scbond_other 2.031 r_mcbond_it 1.682 r_mcbond_other 1.681 r_angle_other_deg 1.182 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 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 1266 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing