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Crystal Structure of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP and 3-hydroxybutyryl-CoA
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 2.55 51.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.938 α = 90 b = 70.938 β = 90 c = 138.613 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 2011-05-11 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 1.8 31.72 94.9 0.054 0.054 14.7 4.3 63474 60265
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 1.8 1.9 89.1 0.29 0.29 2.4 2.3 7806
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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT IN-HOUSE MIR MODEL 1.8 31.72 60245 57176 3069 94.99 0.18064 0.17812 0.1814 0.22843 RANDOM 25.666
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] 0.06 0.06 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.297 r_dihedral_angle_3_deg 17.173 r_dihedral_angle_4_deg 12.517 r_dihedral_angle_1_deg 7.873 r_scangle_it 6.289 r_scbond_it 4.363 r_mcangle_it 2.813 r_angle_refined_deg 2.331 r_mcbond_it 1.863 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.297 r_dihedral_angle_3_deg 17.173 r_dihedral_angle_4_deg 12.517 r_dihedral_angle_1_deg 7.873 r_scangle_it 6.289 r_scbond_it 4.363 r_mcangle_it 2.813 r_angle_refined_deg 2.331 r_mcbond_it 1.863 r_chiral_restr 0.156 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4326 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 238
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement SAINT data reduction SADABS data scaling