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Crystal structure of dipeptidyl peptidase IV in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QJR PDB entry 2QJR
Crystallization Crystal Properties Matthews coefficient Solvent content 2.67 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.429 α = 90 b = 67.141 β = 90 c = 421.529 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 210 2004-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
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 2.4 50 75 0.109 14 3.9 34242 2
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 2.4 2.49 32 0.325 2 1.9 1121
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 2QJR 2.43 50 32550 1685 47.79 0.24586 0.24324 0.249 0.29496 0.2907 RANDOM 81.832
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] -8.11 18.12 -10
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.231 r_dihedral_angle_3_deg 18.521 r_dihedral_angle_4_deg 16.678 r_dihedral_angle_1_deg 6.862 r_scangle_it 1.503 r_angle_refined_deg 1.33 r_scbond_it 0.935 r_angle_other_deg 0.755 r_mcangle_it 0.653 r_mcbond_it 0.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.231 r_dihedral_angle_3_deg 18.521 r_dihedral_angle_4_deg 16.678 r_dihedral_angle_1_deg 6.862 r_scangle_it 1.503 r_angle_refined_deg 1.33 r_scbond_it 0.935 r_angle_other_deg 0.755 r_mcangle_it 0.653 r_mcbond_it 0.555 r_symmetry_vdw_refined 0.444 r_symmetry_vdw_other 0.435 r_nbd_refined 0.244 r_nbd_other 0.242 r_nbtor_refined 0.204 r_xyhbond_nbd_refined 0.203 r_nbtor_other 0.1 r_symmetry_hbond_refined 0.092 r_xyhbond_nbd_other 0.081 r_mcbond_other 0.08 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11926 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 206
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing