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Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with an analog of seryladenylate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 294 PROTEIN WAS CRYSTALLIZED FROM 5-9% MPD, 50 MM MES, PH 5.9, 294 K, HANGING DROP VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 3.14 60.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.713 α = 90 b = 96.713 β = 90 c = 270.302 γ = 120
Symmetry Space Group P 32 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 2005-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 15 90.4 0.06 19.9 3.9 59591 2
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 2.38 94.9 0.24 4.1 3.9
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 MAD THROUGHOUT 2.3 14.93 49301 2567 78.8 0.208 0.206 0.2078 0.248 0.2458 RANDOM 72.35
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.591 r_dihedral_angle_3_deg 15.878 r_dihedral_angle_4_deg 15.678 r_dihedral_angle_1_deg 5.155 r_scangle_it 1.206 r_angle_refined_deg 1.066 r_scbond_it 0.745 r_mcangle_it 0.657 r_mcbond_it 0.382 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.591 r_dihedral_angle_3_deg 15.878 r_dihedral_angle_4_deg 15.678 r_dihedral_angle_1_deg 5.155 r_scangle_it 1.206 r_angle_refined_deg 1.066 r_scbond_it 0.745 r_mcangle_it 0.657 r_mcbond_it 0.382 r_nbtor_refined 0.298 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_refined 0.114 r_chiral_restr 0.074 r_symmetry_hbond_refined 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 7899 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling