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Cyclophilin A complexed with tri-vector ligand 5.
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 2.74 55.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.59 α = 90 b = 52.84 β = 90 c = 87.98 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 2018-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.90001 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 1.29 45.3 98.89 0.062 0.068 0.027 0.999 12.1 6 50202
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 1.29 1.31 98.75 0.602 0.505 1.2
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 1.29 45.3 47575 2533 98.69 0.16488 0.16371 0.18791 0.1928 RANDOM 21.798
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.79 r_dihedral_angle_4_deg 22.347 r_dihedral_angle_3_deg 12.02 r_long_range_B_refined 7.704 r_long_range_B_other 7.701 r_dihedral_angle_1_deg 5.859 r_scangle_other 4.463 r_mcangle_other 3.053 r_mcangle_it 3.029 r_scbond_it 2.852
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.79 r_dihedral_angle_4_deg 22.347 r_dihedral_angle_3_deg 12.02 r_long_range_B_refined 7.704 r_long_range_B_other 7.701 r_dihedral_angle_1_deg 5.859 r_scangle_other 4.463 r_mcangle_other 3.053 r_mcangle_it 3.029 r_scbond_it 2.852 r_scbond_other 2.851 r_angle_refined_deg 2.11 r_mcbond_it 1.99 r_mcbond_other 1.989 r_angle_other_deg 1.069 r_chiral_restr 0.138 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 300 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing