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X-ray crystal structure of C118A RlmN with cross-linked tRNA purified from Escherichia coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG 4000, potassium chloride, magnesium chloride, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 3.77 67.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.664 α = 90 b = 69.821 β = 90.3 c = 149.298 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 CCD MARMOSAIC 300 mm CCD 2014-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 2.85 88.663 99.6 0.132 7.1 6.3 23364
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.9 99.6 6.8
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 THROUGHOUT 2.88 88.663 39727 1700 98.92 0.18365 0.18175 0.1863 0.22811 0.2254 RANDOM 72.823
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] -1.52 0.56 1.09 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.694 r_dihedral_angle_4_deg 18.056 r_dihedral_angle_3_deg 17.107 r_long_range_B_refined 9.429 r_long_range_B_other 9.428 r_scangle_other 7.171 r_dihedral_angle_1_deg 6.899 r_mcangle_it 5.738 r_mcangle_other 5.737 r_scbond_it 4.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.694 r_dihedral_angle_4_deg 18.056 r_dihedral_angle_3_deg 17.107 r_long_range_B_refined 9.429 r_long_range_B_other 9.428 r_scangle_other 7.171 r_dihedral_angle_1_deg 6.899 r_mcangle_it 5.738 r_mcangle_other 5.737 r_scbond_it 4.978 r_scbond_other 4.977 r_mcbond_it 3.824 r_mcbond_other 3.824 r_angle_refined_deg 1.695 r_angle_other_deg 1.178 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5572 Nucleic Acid Atoms 2845 Solvent Atoms 46 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing