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Crystal Structure of the S84A mutant of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP-4-amino-4,6-dideoxyglucose and Coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other IN-HOUSE MIR MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 25% pentaerythritol ethoxylate (3/4 EO/OH), 2% isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.254 α = 90 b = 71.254 β = 90 c = 138.382 γ = 90
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 Bruker Platinum 135 Montel 2011-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 40.73 95.3 0.055 0.055 14.4 4.1 35097 33434
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 86.7 0.189 0.189 3.1 2 3509
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT IN-HOUSE MIR MODEL 2.2 40.73 33423 31748 1675 95.36 0.18766 0.18436 0.24956 0.2343 RANDOM 30.228
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] 0.23 0.23 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.525 r_dihedral_angle_3_deg 18.286 r_dihedral_angle_4_deg 17.143 r_dihedral_angle_1_deg 7.774 r_scangle_it 5.184 r_scbond_it 3.522 r_angle_refined_deg 2.276 r_mcangle_it 2.171 r_mcbond_it 1.304 r_chiral_restr 0.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.525 r_dihedral_angle_3_deg 18.286 r_dihedral_angle_4_deg 17.143 r_dihedral_angle_1_deg 7.774 r_scangle_it 5.184 r_scbond_it 3.522 r_angle_refined_deg 2.276 r_mcangle_it 2.171 r_mcbond_it 1.304 r_chiral_restr 0.168 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4308 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 262
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement SAINT data reduction SADABS data scaling