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Structure of Human Neurolysin (E475Q) in complex with amyloid-beta 35-40 peptide product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.7 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.341 α = 90 b = 131.341 β = 90 c = 195.979 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS3 6M 2015-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.7 109.11 99.2 0.093 0.985 13.7 8.1 47196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.79 99.6 0.6 0.595 3.2 8.4
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 MOLECULAR REPLACEMENT THROUGHOUT 1I1I 2.7 109.11 44843 2329 98.75 0.21203 0.20958 0.2112 0.26049 0.2609 RANDOM 66.215
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] -1.2 -1.2 2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.688 r_dihedral_angle_4_deg 13.448 r_dihedral_angle_3_deg 12.548 r_dihedral_angle_1_deg 5.368 r_long_range_B_refined 2.781 r_long_range_B_other 2.771 r_mcangle_it 1.644 r_mcangle_other 1.644 r_scangle_other 1.214 r_angle_refined_deg 1.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.688 r_dihedral_angle_4_deg 13.448 r_dihedral_angle_3_deg 12.548 r_dihedral_angle_1_deg 5.368 r_long_range_B_refined 2.781 r_long_range_B_other 2.771 r_mcangle_it 1.644 r_mcangle_other 1.644 r_scangle_other 1.214 r_angle_refined_deg 1.102 r_mcbond_it 0.898 r_mcbond_other 0.898 r_angle_other_deg 0.876 r_scbond_it 0.64 r_scbond_other 0.64 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10723 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing