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Crystal structure of Ribosomal-protein-alanine N-acetyltransferase from Brucella melitensis in complex with Acetyl CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J3G native structure, pdb entry 4J3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 Microlytics MCSG1, C7: 200mM CaCl2, 100mM Tris pH 8.5, 25% PEG 4000G 3350, BrabA.17352.a.A1.PS01094 at 20mg/ml, 2.5mM CoA, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.2 44.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.42 α = 90 b = 74.38 β = 91.62 c = 67.55 γ = 90
Symmetry Space Group C 1 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 RIGAKU SATURN 944+ 2012-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 50 99.5 0.069 27.17 10.1 24280 24170 -3 26.445
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 2.05 95.4 0.301 5.74
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 native structure, pdb entry 4J3G 2 41.58 24280 22938 1232 99.54 0.1754 0.1754 0.1728 0.18 0.2248 0.2301 RANDOM 24.201
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] -0.22 -0.22 0.58 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.353 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_3_deg 12.401 r_dihedral_angle_1_deg 6.242 r_mcangle_it 1.555 r_angle_refined_deg 1.444 r_mcbond_it 0.955 r_mcbond_other 0.952 r_angle_other_deg 0.734 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.353 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_3_deg 12.401 r_dihedral_angle_1_deg 6.242 r_mcangle_it 1.555 r_angle_refined_deg 1.444 r_mcbond_it 0.955 r_mcbond_other 0.952 r_angle_other_deg 0.734 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2516 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 56
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction