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X-ray Structural study of quinone reductase II inhibition by compounds with micromolar to nanomolar range IC50 values
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 298 1.3 M ammonium sulfate, 0.1 M Bis-Tris, 0.1 M NaCl, 5 mM DTT, 12 M FAD, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.512 α = 90 b = 83.504 β = 90 c = 106.795 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 100 IMAGE PLATE MAR scanner 300 mm plate 2008-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 65.8 99.2 0.076 44068 43715
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 99
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 1.85 65.8 43567 2197 99.2 0.1941 0.1923 0.1937 0.2296 0.23 RANDOM 23.2745
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] 1.74 0.01 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.453 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_3_deg 12.364 r_dihedral_angle_1_deg 5.887 r_scangle_it 2.95 r_scbond_it 1.801 r_mcangle_it 1.281 r_angle_refined_deg 1.277 r_mcbond_it 0.687 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.453 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_3_deg 12.364 r_dihedral_angle_1_deg 5.887 r_scangle_it 2.95 r_scbond_it 1.801 r_mcangle_it 1.281 r_angle_refined_deg 1.277 r_mcbond_it 0.687 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3614 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 164
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection