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Structure of the human quinone reductase 2 (NQO2) in complex with pacritinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 200 mM sodium sulphate, 2.2 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.454 α = 90 b = 79.22 β = 90 c = 106.23 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 PIXEL DECTRIS EIGER X 16M 2015-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9785 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.4 48.6 95 0.045 0.999 21.11 4.5 97699
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 1.4 1.45 91 0.329 5.3 4.4
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 FOURIER SYNTHESIS THROUGHOUT 5LBU 1.4 48.6 93339 4913 94.82 0.11005 0.10896 0.1086 0.131 0.1304 RANDOM 14.062
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] 0.44 0.25 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.757 r_sphericity_free 29.752 r_dihedral_angle_4_deg 19.468 r_sphericity_bonded 13.608 r_dihedral_angle_3_deg 11.382 r_rigid_bond_restr 7.698 r_dihedral_angle_1_deg 5.759 r_scangle_other 4.833 r_scbond_it 4.488 r_scbond_other 4.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.757 r_sphericity_free 29.752 r_dihedral_angle_4_deg 19.468 r_sphericity_bonded 13.608 r_dihedral_angle_3_deg 11.382 r_rigid_bond_restr 7.698 r_dihedral_angle_1_deg 5.759 r_scangle_other 4.833 r_scbond_it 4.488 r_scbond_other 4.443 r_long_range_B_refined 4.344 r_long_range_B_other 4.098 r_mcangle_other 1.917 r_mcangle_it 1.916 r_mcbond_it 1.633 r_angle_refined_deg 1.609 r_mcbond_other 1.59 r_angle_other_deg 1.204 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.007 r_bond_other_d 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3604 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 198
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing