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Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 2
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 2.93 57.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.905 α = 90 b = 123.442 β = 114.69 c = 145.684 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 2.39 50 95.4 0.076 15.284 3.8 147841
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) 2.39 2.46 69.6 0.525 2.6 7146
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 2.39 50 147788 7412 95.17 0.189 0.187 0.2317 0.239 0.2751 RANDOM 53.154
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] -3 -0.21 3.4 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.922 r_dihedral_angle_4_deg 17.459 r_dihedral_angle_3_deg 15.388 r_dihedral_angle_1_deg 5.023 r_mcangle_it 1.635 r_scangle_it 1.495 r_angle_refined_deg 1.238 r_mcbond_it 1.012 r_scbond_it 0.971 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.922 r_dihedral_angle_4_deg 17.459 r_dihedral_angle_3_deg 15.388 r_dihedral_angle_1_deg 5.023 r_mcangle_it 1.635 r_scangle_it 1.495 r_angle_refined_deg 1.238 r_mcbond_it 1.012 r_scbond_it 0.971 r_nbtor_refined 0.307 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.153 r_xyhbond_nbd_refined 0.119 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23714 Nucleic Acid Atoms Solvent Atoms 1327 Heterogen Atoms 452
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