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Crystal structure of dipeptidyl peptidase IV (DPP IV) from Pseudoxanthomonas mexicana WO24
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ECF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 0.1M HEPES pH7.5, 10% PEG 6000, 5% 2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.63 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.73 α = 90 b = 326.19 β = 90 c = 71 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2012-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.47 55.15 99.9 0.125 0.135 0.049 0.998 14 7.5 125591
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.51 97.5 0.834 0.932 0.404 0.643 2 5
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 MOLECULAR REPLACEMENT THROUGHOUT 2ECF 2.47 40 119191 6289 99.78 0.22066 0.21733 0.2219 0.284 0.2846 RANDOM 44.745
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] 2.98 -2.66 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.445 r_dihedral_angle_4_deg 19.056 r_dihedral_angle_3_deg 17.855 r_dihedral_angle_1_deg 8.11 r_long_range_B_refined 7.203 r_long_range_B_other 7.203 r_mcangle_it 4.983 r_mcangle_other 4.982 r_scangle_other 4.591 r_mcbond_it 3.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.445 r_dihedral_angle_4_deg 19.056 r_dihedral_angle_3_deg 17.855 r_dihedral_angle_1_deg 8.11 r_long_range_B_refined 7.203 r_long_range_B_other 7.203 r_mcangle_it 4.983 r_mcangle_other 4.982 r_scangle_other 4.591 r_mcbond_it 3.169 r_mcbond_other 3.169 r_scbond_it 2.894 r_scbond_other 2.893 r_angle_refined_deg 1.696 r_angle_other_deg 1.052 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22075 Nucleic Acid Atoms Solvent Atoms 609 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XSCALE data scaling PHASER phasing