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Structure of cyclophilin A in complex with 2-chloropyridin-3-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 2.82 56.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.78 α = 90 b = 54.33 β = 90 c = 87.62 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 2M 2014-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
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 1.49 42.78 99.1 0.08 12.1 7.1 33803
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 1.49 1.53 99.4 0.63 2.5 6.7 2486
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 1.49 38.47 32035 1713 98.9 0.17013 0.16856 0.1693 0.19876 0.2002 RANDOM 19.623
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] 0.44 -0.41 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.212 r_dihedral_angle_4_deg 14.623 r_dihedral_angle_3_deg 12.853 r_long_range_B_refined 6.638 r_long_range_B_other 6.636 r_dihedral_angle_1_deg 6.218 r_scangle_other 4.32 r_scbond_it 2.969 r_scbond_other 2.968 r_mcangle_it 2.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.212 r_dihedral_angle_4_deg 14.623 r_dihedral_angle_3_deg 12.853 r_long_range_B_refined 6.638 r_long_range_B_other 6.636 r_dihedral_angle_1_deg 6.218 r_scangle_other 4.32 r_scbond_it 2.969 r_scbond_other 2.968 r_mcangle_it 2.679 r_mcangle_other 2.679 r_angle_refined_deg 2.032 r_mcbond_it 1.812 r_mcbond_other 1.811 r_angle_other_deg 1.123 r_chiral_restr 0.137 r_bond_refined_d 0.023 r_gen_planes_other 0.015 r_gen_planes_refined 0.014 r_bond_other_d 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 250 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing