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Methionyl-tRNA synthetase from Staphylococcus aureus in complex with chlorhexidine and ATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.10 M magnesium acetate, 0.1 M Bis-Tris pH 7.0, 20% w/v PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.409 α = 90 b = 76.059 β = 90 c = 119.046 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2023-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
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 1.67 64.09 96 0.034 0.038 0.016 1 25.8 5.8 66315
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 1.67 1.76 98.6 0.642 0.703 0.283 0.88 6
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 1.67 64.09 62873 3394 95.71 0.18945 0.18811 0.2001 0.21427 0.2264 RANDOM 32.846
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] 0.07 1.54 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.717 r_dihedral_angle_4_deg 13.024 r_dihedral_angle_3_deg 11.782 r_dihedral_angle_1_deg 5.379 r_long_range_B_refined 3.415 r_long_range_B_other 3.24 r_scangle_other 1.772 r_mcangle_it 1.71 r_mcangle_other 1.71 r_angle_refined_deg 1.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.717 r_dihedral_angle_4_deg 13.024 r_dihedral_angle_3_deg 11.782 r_dihedral_angle_1_deg 5.379 r_long_range_B_refined 3.415 r_long_range_B_other 3.24 r_scangle_other 1.772 r_mcangle_it 1.71 r_mcangle_other 1.71 r_angle_refined_deg 1.291 r_scbond_it 1.032 r_scbond_other 1.031 r_mcbond_it 1.016 r_mcbond_other 1.015 r_angle_other_deg 0.915 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4204 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data scaling MOLREP phasing autoPROC data reduction autoPROC data scaling