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Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis (Ground)
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 VAPOR DIFFUSION, HANGING DROP 8.5 293 tri-potassium citrate, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.79 55.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.33 α = 90 b = 103.59 β = 90 c = 177.33 γ = 90
Symmetry Space Group C 2 2 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 2014-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 1.89 40 97.5 0.08 15 6.1 71425
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 1.89 2.04 92 2.4 2.6
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 1.96 40 61427 3254 98.22 0.21789 0.21492 0.2197 0.27463 0.2741 RANDOM 27.541
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] -1.74 -0.99 2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.195 r_dihedral_angle_4_deg 17.383 r_dihedral_angle_3_deg 13.951 r_dihedral_angle_1_deg 6.812 r_long_range_B_refined 6.07 r_long_range_B_other 5.819 r_scangle_other 4.298 r_mcangle_it 3.095 r_mcangle_other 3.095 r_scbond_it 2.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.195 r_dihedral_angle_4_deg 17.383 r_dihedral_angle_3_deg 13.951 r_dihedral_angle_1_deg 6.812 r_long_range_B_refined 6.07 r_long_range_B_other 5.819 r_scangle_other 4.298 r_mcangle_it 3.095 r_mcangle_other 3.095 r_scbond_it 2.816 r_scbond_other 2.816 r_mcbond_it 2.183 r_mcbond_other 2.179 r_angle_refined_deg 1.858 r_angle_other_deg 1.094 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 5481 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing XSCALE data scaling