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Crystal structure of the Bacillus subtilis N-acetyltransferase YlbP protein in complex with Coenzyme-A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 0.01M Cobalt chloride, 0.25M Sodium chloride, 0.1M MES, 1.8M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.21 70.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.572 α = 90 b = 148.572 β = 90 c = 102.29 γ = 120
Symmetry Space Group P 63 2 2
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 MARMOSAIC 300 mm CCD K-B pair biomorph mirrors 2007-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97931 APS 23-ID-D
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 3.2 30 99 0.116 14.3 6.5 11325 11325 -3
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 3.2 3.31 99.6 0.477 3.9 6.6 1104
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 SAD THROUGHOUT 3.2 30 10209 1101 98.94 0.21934 0.21548 0.1988 0.25462 0.2375 RANDOM 76.773
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] 1.63 0.82 1.63 -2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.896 r_dihedral_angle_4_deg 19.488 r_dihedral_angle_3_deg 14.083 r_dihedral_angle_1_deg 4.727 r_scangle_it 3.518 r_scbond_it 2.083 r_angle_refined_deg 1.56 r_mcangle_it 1.305 r_mcbond_it 0.797 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.896 r_dihedral_angle_4_deg 19.488 r_dihedral_angle_3_deg 14.083 r_dihedral_angle_1_deg 4.727 r_scangle_it 3.518 r_scbond_it 2.083 r_angle_refined_deg 1.56 r_mcangle_it 1.305 r_mcbond_it 0.797 r_nbtor_refined 0.316 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.212 r_symmetry_hbond_refined 0.191 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.108 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2541 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing