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Cyclophilin A in complex with Sanglifehrin A analogue (2R,3S,7S,10S,E)-10-(3-aminopropyl)-2,7-dimethylspiro[3,8,11-triaza-1(2,7)-quinolina-5(3,1)-pyridazinacyclopentadecaphanene-13,5'-[1,3]dioxan]-14-ene-4,6,9,12-tetraone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X4N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 28% PEG-3350, 0.1 M Tris-HCl pH 8.8
Crystal Properties Matthews coefficient Solvent content 2.76 55.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.854 α = 90 b = 52.595 β = 90 c = 89.257 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 PILATUS3 S 6M 2022-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.15 45.31 98.8 0.038 0.044 0.022 1 18.9 7.2 71497
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.17 1.342 1.562 0.789 0.712 7.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.15 45.004 71430 3671 98.653 0.132 0.1309 0.1399 0.149 0.1519 19.689
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] -0.899 1.746 -0.847
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.014 r_dihedral_angle_6_deg 13.863 r_lrange_other 12.811 r_dihedral_angle_3_deg 9.7 r_scangle_it 8.466 r_scangle_other 8.462 r_dihedral_angle_2_deg 7.653 r_dihedral_angle_1_deg 6.26 r_scbond_it 6.142 r_scbond_other 6.139
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.014 r_dihedral_angle_6_deg 13.863 r_lrange_other 12.811 r_dihedral_angle_3_deg 9.7 r_scangle_it 8.466 r_scangle_other 8.462 r_dihedral_angle_2_deg 7.653 r_dihedral_angle_1_deg 6.26 r_scbond_it 6.142 r_scbond_other 6.139 r_mcangle_it 6.133 r_mcangle_other 6.129 r_mcbond_it 4.66 r_mcbond_other 4.657 r_rigid_bond_restr 3.903 r_angle_refined_deg 1.86 r_chiral_restr_other 1.107 r_angle_other_deg 0.813 r_nbd_refined 0.261 r_symmetry_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.21 r_symmetry_xyhbond_nbd_other 0.188 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.156 r_nbd_other 0.149 r_chiral_restr 0.108 r_symmetry_nbtor_other 0.089 r_symmetry_nbd_refined 0.027 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1267 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement autoXDS data reduction Aimless data scaling PHASER phasing