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PanDDA analysis group deposition -- PHIP in complex with Z4912742920
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AV9 7av9
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 1.77 30.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.906 α = 90 b = 27.464 β = 100.25 c = 56.444 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 2022-09-24 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 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 30.19 83 0.064 0.07 0.029 0.993 25.8 5.2 33165
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 23.2 0.247 0.343 0.236 0.861 1.3 465
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 7av9 1.19 30.19 31513 1644 82.67 0.1773 0.1759 0.2282 0.2046 0.2482 RANDOM 18.344
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] -0.06 0.47 0.95 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.249 r_dihedral_angle_3_deg 14.137 r_dihedral_angle_4_deg 11.203 r_dihedral_angle_1_deg 6.247 r_mcangle_it 2.571 r_angle_refined_deg 1.687 r_angle_other_deg 1.418 r_mcbond_other 1.319 r_mcbond_it 1.284 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.249 r_dihedral_angle_3_deg 14.137 r_dihedral_angle_4_deg 11.203 r_dihedral_angle_1_deg 6.247 r_mcangle_it 2.571 r_angle_refined_deg 1.687 r_angle_other_deg 1.418 r_mcbond_other 1.319 r_mcbond_it 1.284 r_chiral_restr 0.088 r_bond_refined_d 0.009 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 1003 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing