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Crystal Structure of the double mutant (Y128A and C222A) of Sortase E mutant 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 2.74 55.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.775 α = 90 b = 111.775 β = 90 c = 71.544 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 1.5 41.01 93.3 0.048 0.054 0.024 0.998 12.9 4.4 50982
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 1.5 1.56 86.2 0.618 0.692 0.307 0.782 1.7 5
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 1.5 41.01 48349 2633 71.94 0.14702 0.14499 0.1489 0.18363 0.1848 RANDOM 25.441
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] 0.53 0.53 -1.06
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.93 r_long_range_B_other 15.929 r_scangle_other 12.329 r_dihedral_angle_3_deg 10.939 r_mcangle_it 9.107 r_mcangle_other 9.106 r_scbond_it 8.491 r_scbond_other 8.489 r_dihedral_angle_1_deg 6.861 r_mcbond_it 6.289
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.93 r_long_range_B_other 15.929 r_scangle_other 12.329 r_dihedral_angle_3_deg 10.939 r_mcangle_it 9.107 r_mcangle_other 9.106 r_scbond_it 8.491 r_scbond_other 8.489 r_dihedral_angle_1_deg 6.861 r_mcbond_it 6.289 r_mcbond_other 6.284 r_dihedral_angle_2_deg 5.224 r_rigid_bond_restr 3.667 r_angle_refined_deg 1.642 r_angle_other_deg 0.551 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 2589 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing