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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 28.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.069 α = 90 b = 27.088 β = 100.38 c = 55.915 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 1.18 39.87 74.3 0.055 0.066 0.037 0.996 9.3 2.6 29598
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 1.18 1.24 59.7 0.404 0.554 0.377 0.83 1.2 3375
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 1.18 39.9 28131 1466 74.12 0.175 0.1737 0.2299 0.2008 0.2594 RANDOM 15.027
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] 0.08 0.43 0.63 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.952 r_dihedral_angle_4_deg 14.903 r_dihedral_angle_3_deg 13.29 r_dihedral_angle_1_deg 5.21 r_angle_refined_deg 1.623 r_angle_other_deg 1.552 r_mcangle_it 1.51 r_mcbond_other 0.886 r_mcbond_it 0.877 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.952 r_dihedral_angle_4_deg 14.903 r_dihedral_angle_3_deg 13.29 r_dihedral_angle_1_deg 5.21 r_angle_refined_deg 1.623 r_angle_other_deg 1.552 r_mcangle_it 1.51 r_mcbond_other 0.886 r_mcbond_it 0.877 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 990 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing