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Crystal Structure of human Dipeptidyl Peptidase IV in complex with a pyridopyrimidinedione analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G0G PDB ENTRY 3G0G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 277 22.5% PEG 200mme, 0.1M Bicine pH 7.8 , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.8 56.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.622 α = 90 b = 121.362 β = 114.63 c = 143.257 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 315 2004-04-11 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) 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 2.89 50 96.8 82355 84273 1 1
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 3G0G 2.9 40 77247 4065 96.4 0.2093 0.20666 0.2072 0.25922 0.2598 RANDOM 45.237
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] -1.73 0.52 0.46 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.657 r_dihedral_angle_4_deg 14.35 r_dihedral_angle_3_deg 14.156 r_dihedral_angle_1_deg 4.328 r_angle_refined_deg 1.028 r_chiral_restr 0.073 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.657 r_dihedral_angle_4_deg 14.35 r_dihedral_angle_3_deg 14.156 r_dihedral_angle_1_deg 4.328 r_angle_refined_deg 1.028 r_chiral_restr 0.073 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23642 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 404
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling