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Crystal structure of apo DPP9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EOR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.08 M Na-Cacodilate pH 5.25, 0.16 M Ca-Acetate, 30 % Glycerol, 10 % PEG 8K
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.17 α = 86.56 b = 95.31 β = 102.54 c = 127.196 γ = 102.44
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 EIGER X 16M 2019-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 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 2.9 46.89 98.4 0.087 0.115 0.991 7.24 2.235 92941 50.051
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 2.9 2.97 98.1 0.491 0.645 0.806 2.06 2.299
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 6EOR 2.9 46.89 88289 4647 98.43 0.2264 0.223 0.2262 0.29 0.2896 RANDOM 59.125
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] -1.12 -5.08 5.61 -0.99 -5.08 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.805 r_dihedral_angle_3_deg 17.669 r_dihedral_angle_4_deg 16.715 r_dihedral_angle_1_deg 7.403 r_angle_refined_deg 1.272 r_angle_other_deg 1.061 r_chiral_restr 0.045 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.805 r_dihedral_angle_3_deg 17.669 r_dihedral_angle_4_deg 16.715 r_dihedral_angle_1_deg 7.403 r_angle_refined_deg 1.272 r_angle_other_deg 1.061 r_chiral_restr 0.045 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25524 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 32
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing