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Structure of cyclophilin A in complex with 3-chloropyridin-2-amine
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 2.71 54.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.18 α = 90 b = 53.88 β = 90 c = 85.91 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 1.6 45.65 99.9 0.14 7.9 5.4 26543
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 1.6 1.63 99.9 0.74 2.3 5.7 1327
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 1.6 45.65 25209 1278 99.71 0.16674 0.16525 0.1683 0.19617 0.1997 RANDOM 19.348
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] -0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.132 r_dihedral_angle_4_deg 18.822 r_dihedral_angle_3_deg 11.877 r_dihedral_angle_1_deg 6.915 r_long_range_B_refined 6.234 r_long_range_B_other 6.233 r_scangle_other 4.668 r_scbond_it 3.153 r_scbond_other 3.153 r_mcangle_it 2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.132 r_dihedral_angle_4_deg 18.822 r_dihedral_angle_3_deg 11.877 r_dihedral_angle_1_deg 6.915 r_long_range_B_refined 6.234 r_long_range_B_other 6.233 r_scangle_other 4.668 r_scbond_it 3.153 r_scbond_other 3.153 r_mcangle_it 2.8 r_mcangle_other 2.799 r_angle_refined_deg 1.975 r_mcbond_it 1.951 r_mcbond_other 1.95 r_angle_other_deg 1.089 r_chiral_restr 0.141 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 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 159 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing