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Rational drug design of phenazopyridine derivatives as novel inhibitors of Rev1-CT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 162 mM triammonium citrate and 18% w/v PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.019 α = 90 b = 73.023 β = 90 c = 85.554 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 280 PIXEL DECTRIS EIGER X 9M 2019-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 .9201 NSLS-II 17-ID-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 2.47 29.508 99.6 0.067 0.075 0.028 0.999 13.7 6.4 11712
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 2.47 2.57 0.784 0.857 0.47 0.823 2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3vu7 2.472 29.508 11673 620 99.497 0.203 0.2014 0.2015 0.2375 0.2375 70
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] 3.385 0.161 -3.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.572 r_lrange_other 19.498 r_lrange_it 19.497 r_dihedral_angle_3_deg 18.461 r_dihedral_angle_4_deg 17.527 r_scangle_it 16.702 r_scangle_other 16.698 r_mcangle_it 13.921 r_mcangle_other 13.918 r_scbond_it 12.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.572 r_lrange_other 19.498 r_lrange_it 19.497 r_dihedral_angle_3_deg 18.461 r_dihedral_angle_4_deg 17.527 r_scangle_it 16.702 r_scangle_other 16.698 r_mcangle_it 13.921 r_mcangle_other 13.918 r_scbond_it 12.315 r_scbond_other 12.311 r_mcbond_it 10.496 r_mcbond_other 10.488 r_dihedral_angle_1_deg 8.771 r_angle_other_deg 2.344 r_angle_refined_deg 1.924 r_nbd_other 0.291 r_symmetry_nbd_refined 0.27 r_symmetry_xyhbond_nbd_refined 0.251 r_nbd_refined 0.236 r_symmetry_nbd_other 0.23 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_other 0.112 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.078 r_bond_other_d 0.034 r_bond_refined_d 0.014 r_gen_planes_other 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2546 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing