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Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 BICINE pH 9.0, sodium chloride, PEG MME 550
Crystal Properties Matthews coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.788 α = 90 b = 115.486 β = 90 c = 147.57 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 95 CCD ADSC QUANTUM 270 2012-12-20 M MAD
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 Sym 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 2.46 40 99.6 0.11 12.6 6.6 62234
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 2.46 2.52 99.5 2.1 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.46 40 58784 2980 99.19 0.1866 0.18415 0.1976 0.23339 0.2406 RANDOM 41.04
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] -0.57 2.1 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.207 r_dihedral_angle_4_deg 19.514 r_dihedral_angle_3_deg 18.495 r_long_range_B_other 7.408 r_long_range_B_refined 7.407 r_dihedral_angle_1_deg 7.079 r_scangle_other 5.706 r_mcangle_it 4.471 r_mcangle_other 4.471 r_scbond_it 3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.207 r_dihedral_angle_4_deg 19.514 r_dihedral_angle_3_deg 18.495 r_long_range_B_other 7.408 r_long_range_B_refined 7.407 r_dihedral_angle_1_deg 7.079 r_scangle_other 5.706 r_mcangle_it 4.471 r_mcangle_other 4.471 r_scbond_it 3.6 r_scbond_other 3.597 r_mcbond_it 2.897 r_mcbond_other 2.897 r_angle_refined_deg 1.757 r_angle_other_deg 1.069 r_chiral_restr 0.099 r_bond_refined_d 0.015 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 11216 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement xia2 data processing SHARP phasing ARP model building