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Binding of anti-cancer prodrug CB1954 to the activating enzyme NQO2 revealed by the crystal structure of their complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QR2 PDB ENTRY 1QR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.66M AMM. SULF IN 100MM NA-HEPES PH 7 AND 12MICROM FAD, 1MM DTT
Crystal Properties Matthews coefficient Solvent content 2.2 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.83 α = 90 b = 106.11 β = 90 c = 61.65 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 93 IMAGE PLATE RIGAKU RAXIS IV VARIMAX HF 2005-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 30 99.4 0.08 13.9 6.4 36382 30.54
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 2.11 96.3 0.4 3 4.5
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 (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 PDB ENTRY 1QR2 2 30 34512 1813 99.4 0.196 0.193 0.1974 0.247 0.2402 RANDOM 32.47
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] 3.08 -2.89 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.426 r_dihedral_angle_4_deg 23.974 r_dihedral_angle_3_deg 14.808 r_dihedral_angle_1_deg 7.386 r_scangle_it 4.066 r_scbond_it 2.606 r_angle_refined_deg 1.865 r_mcangle_it 1.782 r_mcbond_it 1.134 r_symmetry_hbond_refined 0.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.426 r_dihedral_angle_4_deg 23.974 r_dihedral_angle_3_deg 14.808 r_dihedral_angle_1_deg 7.386 r_scangle_it 4.066 r_scbond_it 2.606 r_angle_refined_deg 1.865 r_mcangle_it 1.782 r_mcbond_it 1.134 r_symmetry_hbond_refined 0.698 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.309 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.119 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3648 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling