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Crystal Structure of the D94A mutant of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP 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 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.076 α = 90 b = 71.076 β = 90 c = 137.749 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 2011-08-29 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 2.5 40.599 94.4 0.151 0.151 5.9 4 23813 22486
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 2.5 2.6 80.7 0.38 0.38 1.6 1.4 2201
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT IN-HOUSE MIR MODEL 2.5 40.599 22458 21291 1167 94.45 0.19993 0.19574 0.1929 0.27688 0.2712 RANDOM 28.836
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] -0.31 -0.31 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.019 r_dihedral_angle_3_deg 20.148 r_dihedral_angle_4_deg 17.992 r_dihedral_angle_1_deg 7.687 r_scangle_it 3.699 r_scbond_it 2.27 r_angle_refined_deg 2.211 r_mcangle_it 1.561 r_mcbond_it 0.835 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.019 r_dihedral_angle_3_deg 20.148 r_dihedral_angle_4_deg 17.992 r_dihedral_angle_1_deg 7.687 r_scangle_it 3.699 r_scbond_it 2.27 r_angle_refined_deg 2.211 r_mcangle_it 1.561 r_mcbond_it 0.835 r_chiral_restr 0.135 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4309 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 220
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement SAINT data reduction SADABS data scaling