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Porcine dipeptidyl peptidase IV (CD26) in complex with 7-Benzyl-1,3-dimethyl-8-piperazin-1-yl-3,7-dihydro-purine-2,6-dione (BDPX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ORV PDB ENTRY 1ORV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 20% PEG 2000, 0.1 M AMMONIUM SULFATE, 0.1 M TRIS/HCL PH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.48 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.11 α = 112.79 b = 118.96 β = 95.74 c = 133.76 γ = 90.63
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 MARRESEARCH 2004-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 2.07 39.45 97.7 0.054 212238
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 2.07 2.09 96.6 0.444
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-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 1ORV 2.11 39.45 210621 9993 97.7 0.197 0.2028 0.239 0.2432 RANDOM 32.8
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] 6.75 -0.85 -5.12 -2.32 1.65 -4.42
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 2.99 c_scbond_it 2.1 c_mcangle_it 2.09 c_angle_deg 1.6 c_mcbond_it 1.36 c_improper_angle_d 0.93 c_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23864 Nucleic Acid Atoms Solvent Atoms 1646 Heterogen Atoms 712
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction CNS phasing