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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 2.43 49.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.587 α = 90 b = 83.741 β = 90 c = 106.432 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 CCD ADSC QUANTUM 315 2007-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 65.8 97.1 34979 33965
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 95.2 0.062
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 2 65.8 33915 1709 96.97 0.1773 0.1748 0.1746 0.2243 0.2238 RANDOM 20.8321
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] 0.74 0.62 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.169 r_dihedral_angle_4_deg 18.746 r_dihedral_angle_3_deg 13.004 r_dihedral_angle_1_deg 6.276 r_scangle_it 2.803 r_scbond_it 1.728 r_angle_refined_deg 1.306 r_mcangle_it 1.198 r_mcbond_it 0.647 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.169 r_dihedral_angle_4_deg 18.746 r_dihedral_angle_3_deg 13.004 r_dihedral_angle_1_deg 6.276 r_scangle_it 2.803 r_scbond_it 1.728 r_angle_refined_deg 1.306 r_mcangle_it 1.198 r_mcbond_it 0.647 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3628 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 150
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling HKL-2000 data scaling