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Stenotrophomonas maltophilia DPP7 in complex with Asn-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 2.61 52.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.552 α = 90 b = 74.892 β = 94.502 c = 154.647 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) 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 1.92 50.48 99.7 0.186 0.076 0.989 7.4 6.9 119220 14.452
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 1.92 1.95 94.8 1.199 0.485 0.632 2 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 1.92 40.003 119144 6098 99.805 0.205 0.2022 0.2091 0.2478 0.2566 30.137
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] -0.664 0.211 -0.265 0.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.709 r_dihedral_angle_3_deg 15.699 r_dihedral_angle_4_deg 14.819 r_dihedral_angle_1_deg 6.661 r_lrange_it 6.392 r_lrange_other 6.206 r_scangle_it 4.078 r_scangle_other 4.078 r_mcangle_it 3.695 r_mcangle_other 3.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.709 r_dihedral_angle_3_deg 15.699 r_dihedral_angle_4_deg 14.819 r_dihedral_angle_1_deg 6.661 r_lrange_it 6.392 r_lrange_other 6.206 r_scangle_it 4.078 r_scangle_other 4.078 r_mcangle_it 3.695 r_mcangle_other 3.695 r_scbond_it 2.581 r_scbond_other 2.581 r_mcbond_it 2.477 r_mcbond_other 2.476 r_angle_refined_deg 1.554 r_angle_other_deg 1.318 r_nbd_refined 0.208 r_symmetry_nbd_other 0.176 r_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.164 r_nbd_other 0.154 r_symmetry_xyhbond_nbd_refined 0.153 r_symmetry_nbd_refined 0.15 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.073 r_bond_refined_d 0.009 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 10660 Nucleic Acid Atoms Solvent Atoms 1162 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling REFMAC phasing