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Structure of cyclophilin A in complex with 4-chloropyrimidin-5-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 2.76 55.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.48 α = 90 b = 54.4 β = 90 c = 86.13 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 1.45 46 99.3 0.06 5.3 5.3 35840
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 1.45 1.47 99.7 0.58 3.1 5.3
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 1.45 45.99 34058 1737 98.99 0.16113 0.15998 0.1625 0.18349 0.1825 RANDOM 18.288
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.746 r_dihedral_angle_4_deg 18.231 r_dihedral_angle_3_deg 11.605 r_dihedral_angle_1_deg 6.676 r_long_range_B_refined 6.039 r_long_range_B_other 6.038 r_scangle_other 4.634 r_scbond_it 3.119 r_scbond_other 3.117 r_mcangle_other 2.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.746 r_dihedral_angle_4_deg 18.231 r_dihedral_angle_3_deg 11.605 r_dihedral_angle_1_deg 6.676 r_long_range_B_refined 6.039 r_long_range_B_other 6.038 r_scangle_other 4.634 r_scbond_it 3.119 r_scbond_other 3.117 r_mcangle_other 2.944 r_mcangle_it 2.94 r_angle_refined_deg 2.237 r_mcbond_other 1.942 r_mcbond_it 1.94 r_angle_other_deg 1.14 r_chiral_restr 0.155 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 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 146 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing