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A novel bottom-up approach to find lead-compounds in billion-sized libraries
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZC9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 283.15 Morpheus 0.1 Amino acids, 0.1M Buffer system 3 pH 8.5 50% v/v precipitant Mix 1
Crystal Properties Matthews coefficient Solvent content 2.31 46.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.989 α = 90 b = 79.035 β = 90 c = 84.194 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS EIGER X 16M 2022-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.977020 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.94 57.62 99.95 0.142 0.1478 0.04064 0.998 12.97 13.2 21437
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 1.94 2.009 100 1.099 1.142 0.3088 0.778 13.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 1.94 57.62 20397 1033 99.95 0.17995 0.17783 0.1903 0.22164 0.2302 RANDOM 29.793
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] -1.32 1.13 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.755 r_long_range_B_other 10.642 r_long_range_B_refined 10.62 r_scangle_other 8.834 r_scbond_it 6.299 r_scbond_other 6.298 r_dihedral_angle_1_deg 5.953 r_mcangle_it 3.846 r_mcangle_other 3.844 r_mcbond_it 3.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.755 r_long_range_B_other 10.642 r_long_range_B_refined 10.62 r_scangle_other 8.834 r_scbond_it 6.299 r_scbond_other 6.298 r_dihedral_angle_1_deg 5.953 r_mcangle_it 3.846 r_mcangle_other 3.844 r_mcbond_it 3.301 r_mcbond_other 3.277 r_angle_refined_deg 1.406 r_angle_other_deg 0.5 r_chiral_restr 0.07 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2124 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PDB-REDO refinement MxCuBE data collection autoPROC data reduction autoPROC data scaling PHASER phasing