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Xanthomonas citri Methionyl-tRNA synthetase in complex with REP8839
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Tris-HCl, PEG3350, MgCl2
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.161 α = 90 b = 84.418 β = 90 c = 95.823 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 PILATUS 2M 2017-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4586 LNLS W01B-MX2
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 2 48.96 98.7 0.099 0.111 0.048 0.995 10.2 5.1 42403
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 2 2.05 96.4 0.572 0.643 0.287 0.872 4.8
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 (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 6WQ6 2 48.96 40156 2117 98.09 0.2121 0.2097 0.22 0.2552 0.261 RANDOM 33.754
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] 4.27 -4.27 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.714 r_dihedral_angle_4_deg 18.748 r_dihedral_angle_3_deg 16.332 r_dihedral_angle_1_deg 6.627 r_angle_refined_deg 1.808 r_angle_other_deg 1.082 r_chiral_restr 0.104 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.714 r_dihedral_angle_4_deg 18.748 r_dihedral_angle_3_deg 16.332 r_dihedral_angle_1_deg 6.627 r_angle_refined_deg 1.808 r_angle_other_deg 1.082 r_chiral_restr 0.104 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4244 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 28
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction