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Crystal structure of substrate-free human neprilysin E584D.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291.15 Potassium nitrate, sodium bromide, Bis-Tris propane, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.14 α = 90 b = 99.745 β = 106.231 c = 100.119 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 X 16M 2019-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 69.22 99.9 0.992 6.6 6.9 576297
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 0.464 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 6GID 2.1 69.22 83801 4268 99.917 0.221 0.2184 0.2194 0.2614 0.2635 40.443
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] -1.422 -2.141 2.931 -0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.974 r_dihedral_angle_4_deg 14.686 r_dihedral_angle_3_deg 14.516 r_dihedral_angle_1_deg 5.633 r_lrange_it 4.611 r_lrange_other 4.584 r_scangle_it 2.96 r_scangle_other 2.96 r_mcangle_it 2.586 r_mcangle_other 2.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.974 r_dihedral_angle_4_deg 14.686 r_dihedral_angle_3_deg 14.516 r_dihedral_angle_1_deg 5.633 r_lrange_it 4.611 r_lrange_other 4.584 r_scangle_it 2.96 r_scangle_other 2.96 r_mcangle_it 2.586 r_mcangle_other 2.586 r_angle_other_deg 2.349 r_scbond_it 1.749 r_scbond_other 1.749 r_mcbond_it 1.583 r_mcbond_other 1.583 r_angle_refined_deg 1.212 r_symmetry_nbd_other 0.202 r_nbd_other 0.18 r_nbd_refined 0.175 r_nbtor_refined 0.154 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.119 r_metal_ion_refined 0.106 r_symmetry_nbtor_other 0.057 r_chiral_restr 0.045 r_symmetry_xyhbond_nbd_other 0.037 r_bond_other_d 0.036 r_gen_planes_other 0.004 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11031 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing