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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 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.256 α = 90 b = 83.74 β = 90 c = 106.619 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 2007-12-13 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 2.28 65.8 99.9 0.124 23800 23562
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 2.28 2.38 99.8
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 2.28 65.8 23510 1211 99.87 0.1659 0.163 0.1629 0.2195 0.2202 RANDOM 29.5989
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] 1.4 0.02 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.834 r_dihedral_angle_4_deg 19.093 r_dihedral_angle_3_deg 14.157 r_dihedral_angle_1_deg 6.264 r_scangle_it 3.566 r_scbond_it 2.231 r_angle_refined_deg 1.537 r_mcangle_it 1.507 r_mcbond_it 0.792 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.834 r_dihedral_angle_4_deg 19.093 r_dihedral_angle_3_deg 14.157 r_dihedral_angle_1_deg 6.264 r_scangle_it 3.566 r_scbond_it 2.231 r_angle_refined_deg 1.537 r_mcangle_it 1.507 r_mcbond_it 0.792 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3614 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 150
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection