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Crystal structures of human E-NPP 1: bound to N-{[1-(6,7-dimethoxy-5,8-dihydroquinazolin-4-yl)piperidin-4-yl]methyl}sulfuric diamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WET PDB entry 6WET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 7.5 mg/mL protein against 19-22% PEG4000, 240-270 mM trilithium/triammonium/tripotassium citrate
Crystal Properties Matthews coefficient Solvent content 3.26 62.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.278 α = 90 b = 158.993 β = 90 c = 209.23 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 2019-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953736 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.9 47.322 99.9 0.085 0.993 9.9 26 61713
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.98 0.74 0.569 1.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 6WET 2.9 47.28 61629 3122 99.893 0.213 0.2112 0.2132 0.2534 0.2554 62.639
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] 1.945 4.251 -6.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.626 r_dihedral_angle_1_deg 20.716 r_dihedral_angle_4_deg 18.102 r_dihedral_angle_3_deg 16.288 r_lrange_it 11.852 r_lrange_other 11.849 r_mcangle_it 7.04 r_mcangle_other 7.039 r_scangle_it 7.013 r_scangle_other 7.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.626 r_dihedral_angle_1_deg 20.716 r_dihedral_angle_4_deg 18.102 r_dihedral_angle_3_deg 16.288 r_lrange_it 11.852 r_lrange_other 11.849 r_mcangle_it 7.04 r_mcangle_other 7.039 r_scangle_it 7.013 r_scangle_other 7.008 r_mcbond_it 4.436 r_mcbond_other 4.436 r_scbond_it 4.381 r_scbond_other 4.346 r_dihedral_angle_other_3_deg 3.466 r_angle_refined_deg 1.458 r_angle_other_deg 1.233 r_symmetry_nbd_refined 0.208 r_nbd_refined 0.207 r_symmetry_nbd_other 0.18 r_nbd_other 0.18 r_nbtor_refined 0.169 r_metal_ion_refined 0.157 r_xyhbond_nbd_refined 0.148 r_ncsr_local_group_1 0.095 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_refined 0.071 r_symmetry_xyhbond_nbd_other 0.015 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12734 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 278
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing