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Crystal Structure of the double mutant (Y128F and C222A) of Sortase E from Thermobifida fusca
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9IOK Sortase E wild type
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 1.5M Lithium sulfate, 0.1M HEPES-NaOH, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.71 54.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.726 α = 90 b = 111.726 β = 90 c = 70.927 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 S 16M 2023-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
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 1.29 40.85 94.9 0.051 0.058 0.026 0.998 13 4.4 74539
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.34 94.4 0.527 0.592 0.266 0.855 2.6 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.3 40.85 70887 3652 69.22 0.14424 0.14282 0.1438 0.17126 0.1717 RANDOM 15.875
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] 0.1 0.1 -0.21
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.79 r_long_range_B_other 12.78 r_dihedral_angle_3_deg 9.838 r_scangle_other 9.8 r_dihedral_angle_1_deg 6.823 r_scbond_it 6.815 r_scbond_other 6.812 r_mcangle_other 6.673 r_mcangle_it 6.671 r_mcbond_it 4.696
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.79 r_long_range_B_other 12.78 r_dihedral_angle_3_deg 9.838 r_scangle_other 9.8 r_dihedral_angle_1_deg 6.823 r_scbond_it 6.815 r_scbond_other 6.812 r_mcangle_other 6.673 r_mcangle_it 6.671 r_mcbond_it 4.696 r_mcbond_other 4.688 r_dihedral_angle_2_deg 4.392 r_rigid_bond_restr 3.757 r_angle_refined_deg 1.721 r_angle_other_deg 0.718 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2641 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing