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Crystal Structure of human DPP-IV in complex with Anagliptin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BJM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 18% PEG 4000, 15% PEG 1000, 0.15M Na/K-Phosphate, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.16 α = 90 b = 68.99 β = 90 c = 419.6 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 RAYONIX MX225HE 2013-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU SPring-8 BL41XU
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 2.85 49.11 99.9 0.149 12.1 45509
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.92 100
Refinement Statistics Diffraction ID Structure Solution 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 3BJM 2.85 47.67 45508 2275 100 0.227 0.2196 0.288 0.2184 RANDOM 54.87
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]
RMS Deviations Key Refinement Restraint Deviation o_angle_deg 1.85327 o_improper_angle_d 0.37595 o_bond_d 0.01196 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot
RMS Deviations Key Refinement Restraint Deviation o_angle_deg 1.85327 o_improper_angle_d 0.37595 o_bond_d 0.01196 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d o_dihedral_angle_d_na o_dihedral_angle_d_prot o_improper_angle_d_na o_improper_angle_d_prot o_mcbond_it o_mcangle_it o_scbond_it o_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11926 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 239
Software Software Software Name Purpose XDS data scaling MOLREP phasing PRIME-X refinement XDS data reduction XSCALE data scaling