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Crystal structure of dipeptidyl peptidase IV in complex with SYR-472
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 22.2% PEG MME 2000, 0.1M Bicine pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.85 56.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.573 α = 90 b = 122.165 β = 114.57 c = 143.704 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 2007-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.987 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 2.25 50 98.9 0.083 9.5 4 178650
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 2.25 2.3 88.8 0.541 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3G0B 2.24 34.57 169608 8950 97.78 0.1764 0.1743 0.215 0.2143 RANDOM 50.867
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] -0.16 0.25 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.006 r_dihedral_angle_4_deg 18.489 r_dihedral_angle_3_deg 15.866 r_dihedral_angle_1_deg 6.411 r_angle_refined_deg 1.246 r_angle_other_deg 0.742 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.006 r_dihedral_angle_4_deg 18.489 r_dihedral_angle_3_deg 15.866 r_dihedral_angle_1_deg 6.411 r_angle_refined_deg 1.246 r_angle_other_deg 0.742 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23764 Nucleic Acid Atoms Solvent Atoms 1597 Heterogen Atoms 482
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing