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Stenotrophomonas maltophilia DPP7 in complex with Tyr-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 Amm Acetate, 20%w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.54 51.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.85 α = 90 b = 74.32 β = 94.15 c = 153.32 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 CCD RAYONIX MX300HE 2017-04-15 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 1.78 50.04 98.7 0.072 0.095 0.047 0.998 11.5 4 143943 18.981
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 1.78 1.81 87.9 0.872 0.629 0.445 1.2 2.8
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 1.86 40.003 127561 6217 99.777 0.173 0.1714 0.1801 0.2101 0.2154 27.797
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] -0.629 0.213 0.059 0.534
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.491 r_dihedral_angle_4_deg 16.081 r_dihedral_angle_3_deg 14.639 r_dihedral_angle_1_deg 6.511 r_lrange_it 5.93 r_lrange_other 5.768 r_scangle_it 4.575 r_scangle_other 4.575 r_mcangle_it 3.106 r_mcangle_other 3.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.491 r_dihedral_angle_4_deg 16.081 r_dihedral_angle_3_deg 14.639 r_dihedral_angle_1_deg 6.511 r_lrange_it 5.93 r_lrange_other 5.768 r_scangle_it 4.575 r_scangle_other 4.575 r_mcangle_it 3.106 r_mcangle_other 3.106 r_scbond_it 3.049 r_scbond_other 3.048 r_mcbond_it 2.257 r_mcbond_other 2.255 r_angle_refined_deg 1.613 r_angle_other_deg 1.426 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_refined 0.213 r_nbd_other 0.212 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.171 r_symmetry_nbd_refined 0.164 r_xyhbond_nbd_refined 0.161 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_xyhbond_nbd_other 0.007 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 1361 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data scaling REFMAC phasing