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Crystal structure of human neprilysin E584D in complex with C-type natriuretic peptide.
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 iodide, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.267 α = 90 b = 109.267 β = 90 c = 112.579 γ = 120
Symmetry Space Group P 32 2 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 2019-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 2.6 72.44 100 1 17.3 39.9 24386
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 2.6 2.72 0.604
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 2.6 72.44 24353 1287 99.975 0.246 0.2435 0.2449 0.2866 0.2729 91.557
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] 1.816 0.908 1.816 -5.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.303 r_dihedral_angle_3_deg 14.359 r_dihedral_angle_4_deg 13.397 r_dihedral_angle_1_deg 4.852 r_lrange_it 4.753 r_lrange_other 4.752 r_mcangle_it 2.931 r_mcangle_other 2.931 r_scangle_it 2.567 r_scangle_other 2.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.303 r_dihedral_angle_3_deg 14.359 r_dihedral_angle_4_deg 13.397 r_dihedral_angle_1_deg 4.852 r_lrange_it 4.753 r_lrange_other 4.752 r_mcangle_it 2.931 r_mcangle_other 2.931 r_scangle_it 2.567 r_scangle_other 2.567 r_mcbond_it 1.698 r_mcbond_other 1.697 r_scbond_it 1.418 r_scbond_other 1.418 r_angle_refined_deg 1.148 r_angle_other_deg 1.114 r_symmetry_nbd_other 0.162 r_nbd_refined 0.157 r_nbtor_refined 0.151 r_nbd_other 0.134 r_xyhbond_nbd_refined 0.1 r_metal_ion_refined 0.084 r_symmetry_nbtor_other 0.081 r_symmetry_nbd_refined 0.057 r_symmetry_xyhbond_nbd_refined 0.057 r_chiral_restr 0.031 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5475 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing