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Crystal structure of the ribosomal-protein-S18-alanine N-acetyltransferase from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CNT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.01 M tri-sodium citrate, 33% (w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 1.87 34.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.222 α = 93.74 b = 41.785 β = 90.08 c = 46.404 γ = 116.52
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 beryllium lenses 2016-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 1.35 30 95 0.045 38.05 3.9 56272
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 1.35 1.37 90 0.335 3.3 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2CNT 1.35 30 53373 2899 94.83 0.15837 0.15571 0.20902 0.2362 RANDOM 28.192
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] 0.38 1.85 -1.03 0.02 -0.36 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.529 r_sphericity_free 36.421 r_dihedral_angle_4_deg 15.716 r_dihedral_angle_3_deg 14.122 r_sphericity_bonded 12.814 r_dihedral_angle_1_deg 5.696 r_long_range_B_refined 4.557 r_long_range_B_other 3.952 r_scangle_other 3.103 r_scbond_other 2.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.529 r_sphericity_free 36.421 r_dihedral_angle_4_deg 15.716 r_dihedral_angle_3_deg 14.122 r_sphericity_bonded 12.814 r_dihedral_angle_1_deg 5.696 r_long_range_B_refined 4.557 r_long_range_B_other 3.952 r_scangle_other 3.103 r_scbond_other 2.584 r_scbond_it 2.582 r_mcangle_it 2.408 r_mcangle_other 2.407 r_rigid_bond_restr 2.182 r_mcbond_it 1.948 r_mcbond_other 1.946 r_angle_refined_deg 1.662 r_angle_other_deg 1.178 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2463 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing