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Small Dipeptide Analogues developed by Co-crystal Structure of Stenotrophomonas maltophilia Dipeptidyl Peptidase 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DKB 7DKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 20% PEG 8000, 200mM Amm. Acetate, 20% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.55 51.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.2 α = 90 b = 74.25 β = 95.11 c = 154.59 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2016-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.59 34.58 99 0.109 0.128 0.066 0.994 10.4 3.7 47008 35.788
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.63 84.8 0.565 0.361 0.727 2.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7DKB 2.59 30.002 46981 2287 98.895 0.179 0.1754 0.1814 0.2429 0.2456 Random selection 40.889
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] 0.587 -0.075 0.246 -0.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.255 r_dihedral_angle_6_deg 14.913 r_dihedral_angle_1_deg 7.314 r_lrange_it 7.095 r_lrange_other 7.094 r_dihedral_angle_2_deg 6.014 r_scangle_it 5.3 r_scangle_other 5.299 r_mcangle_it 4.628 r_mcangle_other 4.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.255 r_dihedral_angle_6_deg 14.913 r_dihedral_angle_1_deg 7.314 r_lrange_it 7.095 r_lrange_other 7.094 r_dihedral_angle_2_deg 6.014 r_scangle_it 5.3 r_scangle_other 5.299 r_mcangle_it 4.628 r_mcangle_other 4.628 r_scbond_it 3.381 r_scbond_other 3.381 r_mcbond_it 3.007 r_mcbond_other 3.007 r_chiral_restr_other 1.434 r_angle_refined_deg 1.413 r_angle_other_deg 0.535 r_symmetry_xyhbond_nbd_refined 0.302 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.215 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.163 r_nbd_other 0.156 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.061 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10701 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction xia2 data reduction DIALS data reduction PHASER phasing REFMAC refinement Coot model building BUCCANEER model building PHENIX model building