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Secretagogin (mouse) 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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 PEG 3350 (20%), 2 mM CaCl2, 0.1 M Bis-Tris-Propane pH 6.5, 25 mM Tris-HCl pH 8.0, 0.2 M NaI
Crystal Properties Matthews coefficient Solvent content 2.24 45.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.659 α = 90 b = 121.068 β = 90 c = 126.374 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 2020-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97625 MAX IV BioMAX
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 2.35 87.42 99.2 0.098 0.998 11.9 7.3 46202 2.1
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 2.35 2.43 93 0.841 0.529 0.72 2.1 5.9
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 2.35 87.42 43747 2364 99.05 0.19722 0.19444 0.1975 0.24816 0.2473 RANDOM 48.655
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] -1.93 1.08 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.769 r_dihedral_angle_4_deg 19.713 r_dihedral_angle_3_deg 19.204 r_long_range_B_other 9.932 r_long_range_B_refined 9.927 r_scangle_other 6.713 r_dihedral_angle_1_deg 5.425 r_mcangle_it 5.4 r_mcangle_other 5.4 r_scbond_it 4.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.769 r_dihedral_angle_4_deg 19.713 r_dihedral_angle_3_deg 19.204 r_long_range_B_other 9.932 r_long_range_B_refined 9.927 r_scangle_other 6.713 r_dihedral_angle_1_deg 5.425 r_mcangle_it 5.4 r_mcangle_other 5.4 r_scbond_it 4.311 r_scbond_other 4.307 r_mcbond_it 3.653 r_mcbond_other 3.653 r_angle_refined_deg 1.73 r_angle_other_deg 1.053 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 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 8006 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing