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Human dipeptidyl peptidase IV/CD26 in complex with the long-acting inhibitor Omarigliptin (MK-3102)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X70 PDB ENTRY 1X70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20-25% PEG4000, 200 mM sodium acetate, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.01 59.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.94 α = 90 b = 125.777 β = 90 c = 137.085 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 CCD ADSC QUANTUM 210 2009-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 1.9 50 99.8 0.069 10.5 6 160490 160170 -3 -3 25.51
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 1.9 1.97 99.2 0.566 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1X70 1.9 19.15 -3 159855 7998 99.77 0.1678 0.1663 0.1642 0.1974 0.1964 RANDOM 28.99
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] 5.8927 -3.0651 -2.8276
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.85 t_omega_torsion 3.94 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.85 t_omega_torsion 3.94 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11915 Nucleic Acid Atoms Solvent Atoms 1624 Heterogen Atoms 309
Software Software Software Name Purpose StructureStudio data collection REFMAC refinement BUSTER refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing