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Crystal structure of DPP4 in complex with sulphostin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Propietary
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 BICINE: 0.10 M pH:9.00 ; LiSO4: 0.16M ; PEG 2K MME: 24 %w/v
Crystal Properties Matthews coefficient Solvent content 2.77 55.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.92 α = 90 b = 68.208 β = 90 c = 421.06 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M 2022-10-18 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 2.38 210.53 99.9 0.99 14.5 8.2 78066
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 2.38 2.42 0.91
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 2.38 210.53 76954 1109 99.86 0.23625 0.23558 0.2362 0.28547 0.2838 RANDOM 68.05
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 5.93 -7.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.759 r_dihedral_angle_4_deg 15.826 r_dihedral_angle_3_deg 14.628 r_dihedral_angle_1_deg 9.488 r_long_range_B_refined 6.211 r_long_range_B_other 6.21 r_scangle_other 4.108 r_mcangle_it 4.041 r_mcangle_other 4.041 r_mcbond_it 2.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.759 r_dihedral_angle_4_deg 15.826 r_dihedral_angle_3_deg 14.628 r_dihedral_angle_1_deg 9.488 r_long_range_B_refined 6.211 r_long_range_B_other 6.21 r_scangle_other 4.108 r_mcangle_it 4.041 r_mcangle_other 4.041 r_mcbond_it 2.491 r_mcbond_other 2.491 r_scbond_it 2.459 r_scbond_other 2.459 r_angle_refined_deg 1.344 r_angle_other_deg 1.088 r_chiral_restr 0.047 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 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 11937 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 310
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement PHASER phasing