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Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase
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 3.32 62.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.15 α = 90 b = 97.15 β = 90 c = 268.5 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 2004-07-24 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 2.5 50 99.9 0.08 27.9 9.7 51404 -3
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 2.5 2.59 99.8 0.38 4.3 8.1
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 2.51 19.94 46476 2496 95.6 0.202 0.199 0.1987 0.252 0.2458 RANDOM 71.61
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 35.543 r_dihedral_angle_3_deg 16.874 r_dihedral_angle_4_deg 15.702 r_dihedral_angle_1_deg 5.478 r_scangle_it 1.625 r_angle_refined_deg 1.115 r_scbond_it 0.979 r_mcangle_it 0.765 r_mcbond_it 0.439 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.543 r_dihedral_angle_3_deg 16.874 r_dihedral_angle_4_deg 15.702 r_dihedral_angle_1_deg 5.478 r_scangle_it 1.625 r_angle_refined_deg 1.115 r_scbond_it 0.979 r_mcangle_it 0.765 r_mcbond_it 0.439 r_nbtor_refined 0.301 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.078 r_bond_refined_d 0.008 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 7854 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHARP phasing