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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 8.5 283.15 Morpheus 0.09 M Halogens, 0.1M Buffer system 3 pH 8.5 50% v/v precipitant mix 1
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.353 α = 90 b = 39.553 β = 105.492 c = 55.861 γ = 90
Symmetry Space Group P 1 21 1
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 1.42 26.93 95.93 0.07624 0.08237 0.03085 0.998 13.07 7.1 23321
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 1.42 1.471 93.4 0.6479 0.6998 0.262 0.838 2.6 7
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 1.42 26.93 22157 1215 96 0.1725 0.17173 0.1775 0.18634 0.1944 RANDOM 24.278
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] -0.35 0.54 -1.18 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.305 r_long_range_B_other 9.651 r_long_range_B_refined 9.59 r_scangle_other 8.645 r_scbond_it 7.543 r_scbond_other 7.541 r_dihedral_angle_1_deg 5.586 r_mcbond_it 4.464 r_mcangle_it 4.418 r_mcangle_other 4.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.305 r_long_range_B_other 9.651 r_long_range_B_refined 9.59 r_scangle_other 8.645 r_scbond_it 7.543 r_scbond_other 7.541 r_dihedral_angle_1_deg 5.586 r_mcbond_it 4.464 r_mcangle_it 4.418 r_mcangle_other 4.417 r_mcbond_other 4.325 r_angle_refined_deg 1.259 r_angle_other_deg 0.451 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 156 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement PDB-REDO refinement MxCuBE data collection autoPROC data reduction autoPROC data scaling PHASER phasing