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Structure of PPIA in complex with PR dipeptide repeat
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES, 25% PEG1000
Crystal Properties Matthews coefficient Solvent content 2.77 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.319 α = 90 b = 83.319 β = 90 c = 52.455 γ = 120
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 EIGER X 16M 2019-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
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 1.31 42.465 98.7 0.063 21.55 20.06 49424
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 1.31 1.33 91 0.868 17.27
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 5KUL 1.31 42.465 46941 2466 98.7 0.135 0.1335 0.1336 0.1655 0.1659 RANDOM 28.354
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] 2.49 1.24 2.49 -8.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.355 r_dihedral_angle_4_deg 20.581 r_dihedral_angle_3_deg 12.755 r_rigid_bond_restr 7.056 r_dihedral_angle_1_deg 6.175 r_angle_refined_deg 2.137 r_angle_other_deg 1.628 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.355 r_dihedral_angle_4_deg 20.581 r_dihedral_angle_3_deg 12.755 r_rigid_bond_restr 7.056 r_dihedral_angle_1_deg 6.175 r_angle_refined_deg 2.137 r_angle_other_deg 1.628 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1316 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing PDB_EXTRACT data extraction XPREP data scaling