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DPP9 IN COMPLEX WITH LIGAND ICeD-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EOQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 10% PEG 8000
25% glycerol
0.16 M calcium acetate
0.08 M cacodilate pH 6.25
Crystal Properties Matthews coefficient Solvent content 2.91 57.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.789 α = 90 b = 117.439 β = 105.49 c = 163.455 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2019-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.78 157.52 94.4 0.155 1.92 2.7 103766
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.78 3.03 96.4 0.593 2.6
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 6EOQ 2.78 157.52 103032 732 94.4 0.2675 0.267 0.2709 0.3489 0.3548 RANDOM 42.485
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] -3.52 -0.07 2.58 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.048 r_dihedral_angle_4_deg 15.671 r_dihedral_angle_3_deg 14.17 r_dihedral_angle_1_deg 7.35 r_angle_refined_deg 1.604 r_angle_other_deg 1.223 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.048 r_dihedral_angle_4_deg 15.671 r_dihedral_angle_3_deg 14.17 r_dihedral_angle_1_deg 7.35 r_angle_refined_deg 1.604 r_angle_other_deg 1.223 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26773 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing