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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 Properties Matthews coefficient Solvent content 1.73 28.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.376 α = 90 b = 69.376 β = 90 c = 106.391 γ = 120
Symmetry Space Group P 31 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 280 PIXEL DECTRIS EIGER2 X 9M 2019-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97934 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.238 29.073 99.4 0.107 0.997 12.9 9 14749
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.238 2.31 0.774
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 2.24 29.07 14717 771 99.439 0.205 0.204 0.2034 0.221 0.2254 47.319
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] -0.587 -0.293 -0.587 1.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.962 r_dihedral_angle_4_deg 19.043 r_dihedral_angle_3_deg 16.738 r_lrange_it 11.136 r_lrange_other 11.135 r_scangle_it 8.343 r_scangle_other 8.341 r_dihedral_angle_1_deg 8.011 r_mcangle_it 6.951 r_mcangle_other 6.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.962 r_dihedral_angle_4_deg 19.043 r_dihedral_angle_3_deg 16.738 r_lrange_it 11.136 r_lrange_other 11.135 r_scangle_it 8.343 r_scangle_other 8.341 r_dihedral_angle_1_deg 8.011 r_mcangle_it 6.951 r_mcangle_other 6.95 r_scbond_it 5.337 r_scbond_other 5.335 r_mcbond_it 4.653 r_mcbond_other 4.647 r_angle_other_deg 2.289 r_angle_refined_deg 1.824 r_nbd_other 0.253 r_symmetry_nbd_other 0.225 r_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.153 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.034 r_symmetry_xyhbond_nbd_other 0.016 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2470 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing