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Stenotrophomonas maltophilia DPP7 in complex with Val-Tyr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WOL
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 2.43 49.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.49 α = 90 b = 73.33 β = 95.16 c = 151.82 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 2015-10-02 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 1.94 45.75 93.7 0.256 0.275 0.1 0.397 7.9 7.6 100498 18.556
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 1.94 1.97 60.1 1.487 0.576 0.397 1.4 7.5
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 3WOL 2.03 40 91951 4522 97.619 0.203 0.2009 0.2052 0.2454 0.2475 29.45
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] 0.867 0.443 0.819 -1.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.28 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 16.906 r_dihedral_angle_1_deg 6.904 r_lrange_it 5.801 r_lrange_other 5.783 r_scangle_it 4.485 r_scangle_other 4.485 r_mcangle_it 3.215 r_mcangle_other 3.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.28 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 16.906 r_dihedral_angle_1_deg 6.904 r_lrange_it 5.801 r_lrange_other 5.783 r_scangle_it 4.485 r_scangle_other 4.485 r_mcangle_it 3.215 r_mcangle_other 3.215 r_scbond_it 2.891 r_scbond_other 2.891 r_mcbond_it 2.214 r_mcbond_other 2.214 r_angle_refined_deg 1.576 r_angle_other_deg 1.366 r_symmetry_xyhbond_nbd_refined 0.27 r_symmetry_nbd_refined 0.233 r_nbd_refined 0.211 r_nbd_other 0.196 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_other 0.1 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.075 r_chiral_restr 0.073 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 461 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data scaling PHASER phasing