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Stenotrophomonas maltophilia DPP7 in complex with Phe-Tyr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2M Ca Acetate, 20%w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.035 α = 90 b = 74.555 β = 94.437 c = 153.868 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 95 PIXEL DECTRIS EIGER X 16M 2019-01-27 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 1.91 43.13 99.6 0.157 0.17 0.064 0.991 7 6.9 118877 25.163
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 1.91 1.94 93.9 1.012 0.421 0.631 2 6.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7DKB 1.91 40.003 118848 5862 99.685 0.209 0.2073 0.2136 0.2511 0.256 33.301
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] -1.982 -1.009 0.302 1.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.583 r_dihedral_angle_4_deg 17.06 r_dihedral_angle_3_deg 15.024 r_dihedral_angle_1_deg 6.54 r_lrange_it 6.15 r_lrange_other 6.061 r_scangle_it 4.71 r_scangle_other 4.709 r_mcangle_it 3.607 r_mcangle_other 3.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.583 r_dihedral_angle_4_deg 17.06 r_dihedral_angle_3_deg 15.024 r_dihedral_angle_1_deg 6.54 r_lrange_it 6.15 r_lrange_other 6.061 r_scangle_it 4.71 r_scangle_other 4.709 r_mcangle_it 3.607 r_mcangle_other 3.607 r_scbond_it 3.114 r_scbond_other 3.114 r_mcbond_it 2.646 r_mcbond_other 2.643 r_angle_refined_deg 1.575 r_angle_other_deg 1.351 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.207 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.152 r_nbd_other 0.146 r_symmetry_nbd_refined 0.137 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.031 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10658 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling REFMAC phasing