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Crystal structure of DPP8 in complex with 1G244
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, HANGING DROP 6.75 277 0.46 M Na citrate pH 6.75
Crystal Properties Matthews coefficient Solvent content 4.24 70.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.963 α = 90 b = 246.288 β = 90 c = 261.805 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-F 2019-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.2 44.38 99.9 0.146 0.156 0.998 14.51 8.331 87206 74.909
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.28 100 1.41 1.5 0.799 2.05 8.56
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 6EOO 3.2 44.38 82845 4361 99.91 0.1989 0.1968 0.1995 0.2379 0.2363 RANDOM 99.14
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] -2.27 8.7 -6.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.816 r_dihedral_angle_3_deg 14.451 r_dihedral_angle_4_deg 13.602 r_dihedral_angle_1_deg 6.184 r_angle_refined_deg 1.184 r_angle_other_deg 0.853 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.816 r_dihedral_angle_3_deg 14.451 r_dihedral_angle_4_deg 13.602 r_dihedral_angle_1_deg 6.184 r_angle_refined_deg 1.184 r_angle_other_deg 0.853 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20528 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 144
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing