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DPP8 IN COMPLEX WITH LIGAND ICeD-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EOO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 0.46 M NaCitrate pH 6.75
Crystal Properties Matthews coefficient Solvent content 4.52 72.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.288 α = 90 b = 244.937 β = 90 c = 261.487 γ = 90
Symmetry Space Group C 2 2 21
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 0.9998 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 2.69 135.29 96.1 0.064 1.97 3 138235
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 2.69 2.94 97.3 0.58 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6EOO 2.69 135.29 137401 833 96.13 0.1768 0.1765 0.2164 0.1841 RANDOM 64.883
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] -0.63 2.77 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.189 r_dihedral_angle_4_deg 17.882 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_1_deg 7.21 r_angle_refined_deg 1.689 r_angle_other_deg 1.308 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.189 r_dihedral_angle_4_deg 17.882 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_1_deg 7.21 r_angle_refined_deg 1.689 r_angle_other_deg 1.308 r_chiral_restr 0.095 r_bond_refined_d 0.012 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 20709 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 382
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing