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Structure of cyclophilin A in complex with hexahydropyrimidin-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 2.72 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.72 α = 90 b = 52.68 β = 90 c = 89.18 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 1.3 45.36 98.1 0.07 12.7 5 48076
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 1.3 1.32 84.1 0.62 1.7 3.2 2103
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 1.3 45.36 45723 2297 97.71 0.1336 0.13213 0.1354 0.16324 0.1628 RANDOM 19.083
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] 0.05 -0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.974 r_sphericity_free 23.194 r_dihedral_angle_4_deg 19.993 r_sphericity_bonded 10.596 r_dihedral_angle_3_deg 10.535 r_dihedral_angle_1_deg 6.064 r_rigid_bond_restr 6.035 r_scangle_other 5.587 r_long_range_B_refined 5.564 r_long_range_B_other 5.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.974 r_sphericity_free 23.194 r_dihedral_angle_4_deg 19.993 r_sphericity_bonded 10.596 r_dihedral_angle_3_deg 10.535 r_dihedral_angle_1_deg 6.064 r_rigid_bond_restr 6.035 r_scangle_other 5.587 r_long_range_B_refined 5.564 r_long_range_B_other 5.563 r_scbond_other 4.339 r_scbond_it 4.338 r_mcangle_it 3.205 r_mcangle_other 3.203 r_mcbond_it 2.898 r_mcbond_other 2.898 r_angle_refined_deg 2.343 r_angle_other_deg 1.196 r_chiral_restr 0.163 r_bond_refined_d 0.028 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1266 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing