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Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinone inhibitor 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G0B PDB entry 3G0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 277 22.5% PEG MME 200, 0.1M Bicine pH 7.8, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.9 57.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.906 α = 90 b = 122.921 β = 114.77 c = 145.092 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 100 CCD ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0000 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 2.45 50 95.6 0.089 12.667 3.9 136864
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 2.45 2.51 78.3 0.395 2.8 7462
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3G0B 2.45 50 136813 6854 95.39 0.212 0.21 0.2087 0.265 0.2644 RANDOM 50.296
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] -5.83 -0.24 7.1 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.561 r_dihedral_angle_4_deg 16.85 r_dihedral_angle_3_deg 16.302 r_dihedral_angle_1_deg 5.152 r_mcangle_it 1.953 r_scangle_it 1.596 r_angle_refined_deg 1.244 r_mcbond_it 1.212 r_scbond_it 1.075 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.561 r_dihedral_angle_4_deg 16.85 r_dihedral_angle_3_deg 16.302 r_dihedral_angle_1_deg 5.152 r_mcangle_it 1.953 r_scangle_it 1.596 r_angle_refined_deg 1.244 r_mcbond_it 1.212 r_scbond_it 1.075 r_nbtor_refined 0.312 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.142 r_symmetry_vdw_refined 0.138 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23493 Nucleic Acid Atoms Solvent Atoms 738 Heterogen Atoms 544
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing