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PanDDA analysis group deposition -- PHIP in complex with Z4913872963
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 30.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.024 α = 90 b = 27.381 β = 99.49 c = 56.258 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 30.4 84.2 0.045 0.05 0.02 0.994 26.8 5.2 33580
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 24.2 0.326 0.452 0.312 0.868 1.3 464
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 30.41 31897 1683 84.02 0.2558 0.2551 0.2607 0.2685 0.2727 RANDOM 17.333
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] -0.04 0.2 0.88 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.295 r_dihedral_angle_1_deg 5.26 r_dihedral_angle_2_deg 4.074 r_mcangle_it 1.897 r_angle_refined_deg 1.674 r_mcbond_it 1.313 r_mcbond_other 1.312 r_angle_other_deg 1.268 r_chiral_restr 0.077 r_bond_refined_d 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.295 r_dihedral_angle_1_deg 5.26 r_dihedral_angle_2_deg 4.074 r_mcangle_it 1.897 r_angle_refined_deg 1.674 r_mcbond_it 1.313 r_mcbond_other 1.312 r_angle_other_deg 1.268 r_chiral_restr 0.077 r_bond_refined_d 0.016 r_gen_planes_other 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1003 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing