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PanDDA analysis group deposition -- PHIP in complex with Z1004277578
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 1.78 30.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.995 α = 90 b = 27.47 β = 100.04 c = 56.483 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 1.15 55.66 72.9 0.07 0.076 0.03 0.996 14.6 5.3 32310
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.17 5.1 2.064 2.919 2.064 1 113
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 1.15 55.62 30196 1594 71.8 0.1751 0.1739 0.2216 0.1979 0.2426 RANDOM 20.547
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] -0.26 0.46 1.29 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.455 r_dihedral_angle_3_deg 14.273 r_dihedral_angle_4_deg 11 r_dihedral_angle_1_deg 5.957 r_mcangle_it 3.683 r_mcbond_other 1.783 r_mcbond_it 1.739 r_angle_refined_deg 1.529 r_angle_other_deg 1.369 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.455 r_dihedral_angle_3_deg 14.273 r_dihedral_angle_4_deg 11 r_dihedral_angle_1_deg 5.957 r_mcangle_it 3.683 r_mcbond_other 1.783 r_mcbond_it 1.739 r_angle_refined_deg 1.529 r_angle_other_deg 1.369 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1003 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing