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Crystal structure of DPP9 Ser730Ala in complex with sulphostin.
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, HANGING DROP 293 PEG2000 MME 20% (w/v), 0.1 M Tris pH 6.75
Crystal Properties Matthews coefficient Solvent content 2.5 50.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.613 α = 65.15 b = 106.531 β = 70.72 c = 121.27 γ = 76.35
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 2022-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99998 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.89 83.24 96.2 0.99 6 2.2 288843
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.93 0.78
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.89 83.24 286483 2336 96.11 0.17691 0.17672 0.1853 0.19945 0.2058 RANDOM 38.475
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] 1.77 -0.47 -2.26 -2.26 0.88 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.605 r_dihedral_angle_4_deg 18.984 r_dihedral_angle_3_deg 12.36 r_dihedral_angle_1_deg 7.252 r_long_range_B_refined 5.423 r_long_range_B_other 5.353 r_scangle_other 3.559 r_mcangle_it 3.13 r_mcangle_other 3.129 r_scbond_it 2.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.605 r_dihedral_angle_4_deg 18.984 r_dihedral_angle_3_deg 12.36 r_dihedral_angle_1_deg 7.252 r_long_range_B_refined 5.423 r_long_range_B_other 5.353 r_scangle_other 3.559 r_mcangle_it 3.13 r_mcangle_other 3.129 r_scbond_it 2.161 r_scbond_other 2.161 r_mcbond_it 1.922 r_mcbond_other 1.921 r_angle_refined_deg 1.321 r_angle_other_deg 1.163 r_chiral_restr 0.059 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27246 Nucleic Acid Atoms Solvent Atoms 2283 Heterogen Atoms 288
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement PHASER phasing