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Crystal Structure of Human Dipeptidase 3 in Complex with Fab of SC-003
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 0.1 M calcium acetate, 0.1 M sodium acetate pH 4.5, 10% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.31 46.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.03 α = 90 b = 167.03 β = 90 c = 116.38 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 297 PIXEL DECTRIS PILATUS 6M 2018-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.84 40.12 96.2 0.091 20 10.2 42049
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 2.89 0.356
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6VGO 2.84 40.12 42033 2073 96.2 0.193 0.19 0.248 0.2265 RANDOM 80.94
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] -12.853 -12.853 25.7059
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.55 t_omega_torsion 3.45 t_angle_deg 1.12 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.55 t_omega_torsion 3.45 t_angle_deg 1.12 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12070 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing