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Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate 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 20 % (m/v) PEG 8000, 0.2 M tri-potassium citrate, microgravity environment in the Kibo, ISS
Crystal Properties Matthews coefficient Solvent content 2.84 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.13 α = 90 b = 103.35 β = 90 c = 176.52 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 100 PIXEL DECTRIS PILATUS 6M-F 2014-11-25 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 1.5 49.56 99.9 0.049 0.053 0.02 0.999 17.7 6.5 144097 2 18.58
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 1.5 1.53 98.3 0.674 0.764 0.352 0.688 2.1 4.4
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 1.5 49.56 136886 7155 99.84 0.17142 0.1702 0.1789 0.19418 0.2007 RANDOM 23.543
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] -0.63 -0.22 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.493 r_dihedral_angle_4_deg 19.252 r_dihedral_angle_3_deg 13.177 r_dihedral_angle_1_deg 6.594 r_long_range_B_refined 5.507 r_long_range_B_other 5.31 r_scangle_other 4.314 r_scbond_it 2.903 r_scbond_other 2.902 r_mcangle_it 2.534
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.493 r_dihedral_angle_4_deg 19.252 r_dihedral_angle_3_deg 13.177 r_dihedral_angle_1_deg 6.594 r_long_range_B_refined 5.507 r_long_range_B_other 5.31 r_scangle_other 4.314 r_scbond_it 2.903 r_scbond_other 2.902 r_mcangle_it 2.534 r_mcangle_other 2.534 r_mcbond_it 1.812 r_mcbond_other 1.811 r_angle_refined_deg 1.772 r_angle_other_deg 1.526 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 5609 Nucleic Acid Atoms Solvent Atoms 825 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement DIALS data scaling xia2 data reduction REFMAC phasing