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Cyclophilin A complexed with the tri-vector ligand 8.
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 2.82 56.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.621 α = 90 b = 54.535 β = 90 c = 87.486 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 0.979500 Diamond I04
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 1.597 87.486 99.9 0.07 0.08 0.043 0.998 13.5 6.3 27755
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 1.597 1.625 100 0.621 0.689 0.366 0.886 2.4 6.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5NOY 1.6 46.28 26324 1431 99.92 0.15449 0.15254 0.19071 0.2074 RANDOM 29.126
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] 0.05 -0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.14 r_dihedral_angle_4_deg 18.812 r_dihedral_angle_3_deg 12.206 r_long_range_B_refined 9.364 r_long_range_B_other 9.351 r_dihedral_angle_1_deg 6.22 r_scangle_other 6.07 r_mcangle_other 3.998 r_mcangle_it 3.949 r_scbond_it 3.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.14 r_dihedral_angle_4_deg 18.812 r_dihedral_angle_3_deg 12.206 r_long_range_B_refined 9.364 r_long_range_B_other 9.351 r_dihedral_angle_1_deg 6.22 r_scangle_other 6.07 r_mcangle_other 3.998 r_mcangle_it 3.949 r_scbond_it 3.873 r_scbond_other 3.866 r_mcbond_it 2.582 r_mcbond_other 2.479 r_angle_refined_deg 1.996 r_angle_other_deg 1.26 r_chiral_restr 0.144 r_bond_refined_d 0.022 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 225 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing