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Crystal structures of human E-NPP 1: bound to N-{4-[(7-methoxyquinolin-4-yl)oxy]phenyl}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 3.36 63.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.131 α = 90 b = 161.578 β = 90 c = 209.978 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 2019-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953730 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 2.73 47.967 100 0.105 0.99 8.4 11.8 76020
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 2.73 2.79 0.765 0.548 1.3
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 2.73 47.92 75942 3771 99.955 0.212 0.2102 0.2167 0.2409 0.2464 51.507
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] 0.982 2.553 -3.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_1_deg 21.176 r_dihedral_angle_4_deg 17.777 r_dihedral_angle_3_deg 15.441 r_lrange_other 10.499 r_lrange_it 10.497 r_scangle_other 5.637 r_scangle_it 5.636 r_mcangle_it 5.385 r_mcangle_other 5.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_1_deg 21.176 r_dihedral_angle_4_deg 17.777 r_dihedral_angle_3_deg 15.441 r_lrange_other 10.499 r_lrange_it 10.497 r_scangle_other 5.637 r_scangle_it 5.636 r_mcangle_it 5.385 r_mcangle_other 5.385 r_scbond_other 3.435 r_scbond_it 3.434 r_mcbond_it 3.29 r_mcbond_other 3.289 r_angle_refined_deg 1.393 r_angle_other_deg 1.187 r_symmetry_xyhbond_nbd_refined 0.245 r_nbd_other 0.23 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.2 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.139 r_metal_ion_refined 0.113 r_ncsr_local_group_1 0.089 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_symmetry_xyhbond_nbd_other 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12688 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 308
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing