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Crystal structure of Ribosomal-protein-alanine N-acetyltransferase from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J8M pdb entry 2J8M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Microlytics MCSG1, 200mM ammoinum sulfate, 100mM HEPES/NaOH pH 7.5, 25% PEG 3350, BrabA.17352.a.A1.PS01094 at 20mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 1.98 37.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.11 α = 86.55 b = 57 β = 88.15 c = 73.42 γ = 88.76
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 RIGAKU SATURN 944+ 2012-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 1.75 50 97.4 0.058 16.27 3.9 63809 62171 -3 25.624
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 1.75 1.8 96 0.457 2.81
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2J8M 1.75 46.32 63809 62171 3139 97.43 0.1727 0.1727 0.1706 0.1794 0.2119 0.2172 RANDOM 21.7738
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] 0.35 -0.63 0.66 0.39 -0.79 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_dihedral_angle_4_deg 18.875 r_dihedral_angle_3_deg 12.306 r_dihedral_angle_1_deg 6.253 r_mcangle_it 1.838 r_angle_refined_deg 1.323 r_mcbond_it 1.177 r_mcbond_other 1.176 r_angle_other_deg 0.711 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_dihedral_angle_4_deg 18.875 r_dihedral_angle_3_deg 12.306 r_dihedral_angle_1_deg 6.253 r_mcangle_it 1.838 r_angle_refined_deg 1.323 r_mcbond_it 1.177 r_mcbond_other 1.176 r_angle_other_deg 0.711 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5043 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms 53
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction