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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 292.15 Morpheus 0.09M Halogens, 0.1M Buffer System 2 pH6.5, 50% v/v Precipitant Mix 2
Crystal Properties Matthews coefficient Solvent content 2.1 41.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.1 α = 90 b = 44.587 β = 90 c = 78.907 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 2021-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976260 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 1.33 38.85 99.87 0.06058 0.06315 0.01762 0.999 18.97 12.7 29986
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 1.33 1.378 99.46 0.8042 0.837 0.2289 0.913 2.62 12.9
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 1.33 38.85 28623 1484 99.87 0.18759 0.18654 0.1921 0.20806 0.2181 RANDOM 23.77
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] 2.99 -0.44 -2.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.449 r_long_range_B_refined 7.274 r_long_range_B_other 7.258 r_scangle_other 6.476 r_dihedral_angle_1_deg 5.469 r_scbond_other 5.082 r_scbond_it 5.08 r_mcangle_other 2.286 r_mcangle_it 2.283 r_mcbond_other 1.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.449 r_long_range_B_refined 7.274 r_long_range_B_other 7.258 r_scangle_other 6.476 r_dihedral_angle_1_deg 5.469 r_scbond_other 5.082 r_scbond_it 5.08 r_mcangle_other 2.286 r_mcangle_it 2.283 r_mcbond_other 1.884 r_mcbond_it 1.881 r_angle_refined_deg 0.999 r_angle_other_deg 0.392 r_chiral_restr 0.05 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1062 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing