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Crystal structure of dipeptidyl peptidase 11 (DPP11) with SH-5 from Porphyromonas gingivalis (Space)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 8.5 293 19 %(m/v) PEG 8000,0.18 M magnesium formate, 0.5 mM SH-5, 5 % (v/v) DMSO
Crystal Properties Matthews coefficient Solvent content 2.79 55.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.337 α = 90 b = 116.96 β = 90 c = 148.2 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 PIXEL DECTRIS PILATUS3 S 6M 2016-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 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 2.39 116.94 99.8 0.156 0.169 0.063 0.99 9.2 6.9 70956 2 30.999
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 2.39 2.43 97.8 1.283 1.38 0.502 0.692 7.2
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 4Y04 2.39 39.65 67329 3516 99.75 0.20477 0.20228 0.2083 0.25275 0.2518 RANDOM 42.637
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] 1.93 0.34 -2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.09 r_dihedral_angle_3_deg 19.631 r_dihedral_angle_4_deg 19.18 r_long_range_B_refined 7.476 r_long_range_B_other 7.476 r_dihedral_angle_1_deg 7.239 r_scangle_other 5.68 r_mcangle_it 4.788 r_mcangle_other 4.788 r_scbond_it 3.669
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.09 r_dihedral_angle_3_deg 19.631 r_dihedral_angle_4_deg 19.18 r_long_range_B_refined 7.476 r_long_range_B_other 7.476 r_dihedral_angle_1_deg 7.239 r_scangle_other 5.68 r_mcangle_it 4.788 r_mcangle_other 4.788 r_scbond_it 3.669 r_scbond_other 3.669 r_mcbond_it 3.177 r_mcbond_other 3.174 r_angle_refined_deg 1.56 r_angle_other_deg 1.281 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 11216 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data reduction