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Crystal structure of Mycobacterium smegmatis methionyl-tRNA synthetase in complex with methionine and adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A8H PDB ENTRY 1A8H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.2 M NAH2PO4, 800 MM K2HPO4, 200 MM LI2SO4, 100 MM CAPS, PH 7.0, VAPOR DIFFUSION, HANGING DROPS, TEMPERATURE 293 K
Crystal Properties Matthews coefficient Solvent content 3.2 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.95 α = 90 b = 138.91 β = 124.84 c = 123.31 γ = 90
Symmetry Space Group C 1 2 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 CCD MARRESEARCH MULTILAYER MIRROR 2008-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 30 97.8 0.09 11.8 4.1 93306 2 39.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 96.1 0.38 3.2 3.8
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 PDB ENTRY 1A8H 2.3 30 88634 4670 97.7 0.219 0.218 0.2136 0.249 0.2443 RANDOM 23.9
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] 1.43 -0.39 -0.82 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.638 r_dihedral_angle_4_deg 12.955 r_dihedral_angle_3_deg 12.422 r_dihedral_angle_1_deg 4.134 r_angle_refined_deg 0.886 r_scangle_it 0.719 r_mcangle_it 0.416 r_scbond_it 0.398 r_mcbond_it 0.223 r_symmetry_vdw_refined 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.638 r_dihedral_angle_4_deg 12.955 r_dihedral_angle_3_deg 12.422 r_dihedral_angle_1_deg 4.134 r_angle_refined_deg 0.886 r_scangle_it 0.719 r_mcangle_it 0.416 r_scbond_it 0.398 r_mcbond_it 0.223 r_symmetry_vdw_refined 0.096 r_xyhbond_nbd_refined 0.075 r_symmetry_hbond_refined 0.06 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11638 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing