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Secretagogin (human) in complex with its target peptide from SNAP-25
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EMA 1EMA, 8BAN experimental model PDB 8BAN 1EMA, 8BAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.2 M Na-acetate
20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.544 α = 90 b = 120.439 β = 90 c = 124.066 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 110 PIXEL DECTRIS EIGER X 16M Toroidal Mirrors 2020-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97996 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 41.36 99.8 0.103 0.079 0.996 9.5 4.5 47592 1.9 31.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.7 0.702 0.545 0.601 4.6
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 1EMA, 8BAN 2.3 41.36 45084 2449 99.62 0.19149 0.18772 0.1897 0.26156 0.2596 RANDOM 40.713
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] -1.23 1.91 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 16.525 r_long_range_B_refined 7.36 r_long_range_B_other 7.355 r_dihedral_angle_1_deg 6.334 r_scangle_other 5.165 r_mcangle_it 3.744 r_mcangle_other 3.744 r_scbond_it 3.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 16.525 r_long_range_B_refined 7.36 r_long_range_B_other 7.355 r_dihedral_angle_1_deg 6.334 r_scangle_other 5.165 r_mcangle_it 3.744 r_mcangle_other 3.744 r_scbond_it 3.244 r_scbond_other 3.242 r_mcbond_it 2.503 r_mcbond_other 2.5 r_angle_refined_deg 1.485 r_angle_other_deg 0.964 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 8139 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing