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Crystal Structure of Human DPP4 in complex with a benzimidazole derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 277 22.5% PEG 2000mme, 0.1M Bicine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.74 55.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.086 α = 90 b = 123.01 β = 114.84 c = 144.651 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC 2003-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3
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 2.5 50 98.9 0.068 11.2 133909
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 2.5 2.59 99.4 0.531 13334
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 THROUGHOUT 2.49 32.8 133885 6730 98.26 0.202 0.2 0.2337 0.244 0.2698 RANDOM 50.879
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] -1.45 1.05 2.13 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.964 r_dihedral_angle_4_deg 17.026 r_dihedral_angle_3_deg 16.156 r_dihedral_angle_1_deg 5.344 r_mcangle_it 1.648 r_scangle_it 1.459 r_angle_refined_deg 1.239 r_mcbond_it 1.025 r_scbond_it 0.962 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.964 r_dihedral_angle_4_deg 17.026 r_dihedral_angle_3_deg 16.156 r_dihedral_angle_1_deg 5.344 r_mcangle_it 1.648 r_scangle_it 1.459 r_angle_refined_deg 1.239 r_mcbond_it 1.025 r_scbond_it 0.962 r_nbtor_refined 0.312 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.168 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23752 Nucleic Acid Atoms Solvent Atoms 676 Heterogen Atoms 364
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction