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Structure of cyclophilin A in complex with 3-amino-1H-pyridin-2-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LUD
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 2.73 54.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.09 α = 90 b = 52.49 β = 90 c = 89.22 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 2015-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.35 45.25 99.2 0.06 14.5 5.1 43795
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 96 0.56 2.5 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 5LUD 1.35 45.24 41612 2125 98.95 0.13294 0.13135 0.1383 0.16478 0.1702 RANDOM 15.096
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 -0.08 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.43 r_dihedral_angle_4_deg 20.984 r_sphericity_free 18.73 r_dihedral_angle_3_deg 11.048 r_sphericity_bonded 8.467 r_dihedral_angle_1_deg 6.148 r_rigid_bond_restr 5.794 r_scangle_other 3.563 r_scbond_it 3.326 r_scbond_other 3.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.43 r_dihedral_angle_4_deg 20.984 r_sphericity_free 18.73 r_dihedral_angle_3_deg 11.048 r_sphericity_bonded 8.467 r_dihedral_angle_1_deg 6.148 r_rigid_bond_restr 5.794 r_scangle_other 3.563 r_scbond_it 3.326 r_scbond_other 3.323 r_long_range_B_refined 3.248 r_long_range_B_other 3.247 r_angle_refined_deg 2.395 r_mcangle_other 2.217 r_mcangle_it 2.215 r_mcbond_it 2.033 r_mcbond_other 2.031 r_angle_other_deg 1.179 r_chiral_restr 0.162 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_bond_other_d 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1266 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing