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Crystal Structure of human dipeptidyl peptidase IV in complex with a decapeptide (tNPY) at 2.3 Ang. Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R9M PDB Entry: 1R9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.25 298 PEG 2000, Bicine, pH 8.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.606 α = 90 b = 122.701 β = 114.88 c = 145.405 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 173 CCD ADSC QUANTUM 4 2003-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.01 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 23270 0.075 0.054 11.7 2 161260 161260 1 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 2.3 2.36 94.2 0.429 1.8 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry: 1R9M 2.3 41.17 161260 153134 8078 100 0.2127 0.21065 0.2514 RANDOM 47.6
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] -3.14 -1.17 3.08 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.607 r_dihedral_angle_4_deg 18.533 r_dihedral_angle_3_deg 17.555 r_dihedral_angle_1_deg 6.406 r_scangle_it 1.708 r_angle_refined_deg 1.276 r_scbond_it 1.09 r_mcangle_it 0.769 r_mcbond_it 0.445 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.607 r_dihedral_angle_4_deg 18.533 r_dihedral_angle_3_deg 17.555 r_dihedral_angle_1_deg 6.406 r_scangle_it 1.708 r_angle_refined_deg 1.276 r_scbond_it 1.09 r_mcangle_it 0.769 r_mcbond_it 0.445 r_nbtor_refined 0.308 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_refined 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 24028 Nucleic Acid Atoms Solvent Atoms 1249 Heterogen Atoms 350
Software Software Software Name Purpose REFMAC refinement CCP4 data scaling AMoRE phasing