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PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z198194396 synthetic derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5RJI 5RJI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 20% PEG 8000, 0.04M POTASSIUM PHOSPHATE
Crystal Properties Matthews coefficient Solvent content 1.71 28.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.269 α = 90 b = 27.125 β = 100.13 c = 55.64 γ = 90
Symmetry Space Group C 1 2 1
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 2020-09-16 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9127 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.19 54.76 90.6 0.046 0.057 0.033 0.996 8.3 2.6 34986
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.21 48.3 1.232 1.737 1.224 0.228 1.2 880
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 FOURIER SYNTHESIS THROUGHOUT 5RJI 1.19 54.77 32975 1711 89.59 0.1837 0.1826 0.2414 0.2042 0.2514 RANDOM 18.626
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] -0.15 -0.02 1.19 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.612 r_dihedral_angle_4_deg 13.303 r_dihedral_angle_3_deg 13.264 r_dihedral_angle_1_deg 5.225 r_mcangle_it 1.95 r_angle_refined_deg 1.709 r_angle_other_deg 1.571 r_mcbond_other 1.135 r_mcbond_it 1.132 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.612 r_dihedral_angle_4_deg 13.303 r_dihedral_angle_3_deg 13.264 r_dihedral_angle_1_deg 5.225 r_mcangle_it 1.95 r_angle_refined_deg 1.709 r_angle_other_deg 1.571 r_mcbond_other 1.135 r_mcbond_it 1.132 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 990 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing