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Xanthomonas citri Methionyl-tRNA synthetase (apo)
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 0.1 M Tris-HCl, 28 - 32% PEG4000, 0.2 M MgCl2, 0.45 % Polyvinylpyrrolidone K15
Crystal Properties Matthews coefficient Solvent content 1.91 35.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.017 α = 90 b = 95.253 β = 90.52 c = 84.08 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 100 PIXEL DECTRIS PILATUS 2M 2017-04-07 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 47.83 97 0.107 0.127 0.069 0.996 8.6 3.3 76238
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 2.04 95 0.918 1.107 0.609 0.574 3.1
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 47.83 72445 3766 94.31 0.1874 0.185 0.1899 0.2301 0.2334 RANDOM 32.944
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] 44.92 9.17 -25.19 -19.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.329 r_dihedral_angle_4_deg 19.277 r_dihedral_angle_3_deg 15.978 r_dihedral_angle_1_deg 6.438 r_angle_refined_deg 1.657 r_angle_other_deg 1.437 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.329 r_dihedral_angle_4_deg 19.277 r_dihedral_angle_3_deg 15.978 r_dihedral_angle_1_deg 6.438 r_angle_refined_deg 1.657 r_angle_other_deg 1.437 r_chiral_restr 0.084 r_bond_refined_d 0.015 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 8488 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction