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The structure of DPP-4 in complex with piperidine fused imidazopyridine 34
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 PEG 4000, SODIUM ACETATE, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 59.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.12 α = 90 b = 125.496 β = 90 c = 136.902 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 315 2005-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.00 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 30 99.7 0.095 7.5 6.8 137116 -3 30.1
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 2.08 98.1 0.494 1.3 5.6 13341
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 1X70 2 30 130096 6880 99.66 0.17271 0.17102 0.1726 0.20485 0.2053 RANDOM 35.435
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] -1.83 0.43 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.136 r_dihedral_angle_4_deg 19.067 r_dihedral_angle_3_deg 12.818 r_dihedral_angle_1_deg 6.064 r_scangle_it 2.706 r_scbond_it 1.674 r_angle_refined_deg 1.253 r_mcangle_it 1.03 r_mcbond_it 0.545 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.136 r_dihedral_angle_4_deg 19.067 r_dihedral_angle_3_deg 12.818 r_dihedral_angle_1_deg 6.064 r_scangle_it 2.706 r_scbond_it 1.674 r_angle_refined_deg 1.253 r_mcangle_it 1.03 r_mcbond_it 0.545 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.191 r_symmetry_metal_ion_refined 0.154 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.087 r_symmetry_hbond_refined 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11930 Nucleic Acid Atoms Solvent Atoms 1206 Heterogen Atoms 355
Software Software Software Name Purpose ADSC data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing