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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 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.685 α = 90 b = 83.88 β = 90 c = 107.209 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) 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 2.4 66.08 99.8 0.125 8.8 7.2 20400
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 2.4 2.49 99 0.403 6.1 1995
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 2.41 50 20353 1043 99.53 0.167 0.1635 0.1632 0.2345 0.2301 RANDOM 31.3407
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] 0.34 1.09 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.92 r_dihedral_angle_4_deg 19.474 r_dihedral_angle_3_deg 14.343 r_dihedral_angle_1_deg 6.833 r_scangle_it 3.356 r_scbond_it 2.111 r_angle_refined_deg 1.951 r_mcangle_it 1.566 r_mcbond_it 0.839 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.92 r_dihedral_angle_4_deg 19.474 r_dihedral_angle_3_deg 14.343 r_dihedral_angle_1_deg 6.833 r_scangle_it 3.356 r_scbond_it 2.111 r_angle_refined_deg 1.951 r_mcangle_it 1.566 r_mcbond_it 0.839 r_chiral_restr 0.118 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3648 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 152
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection PHASER phasing