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Crystal structure of the N-terminal domain of tetrahydrodipicolinate acetyltransferase from Staphylococcus aureus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 2.4M Sodium malonate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.93 68.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.503 α = 90 b = 76.503 β = 90 c = 93.862 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 CUSTOM-MADE 2007-08-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97921, 0.97942 APS 19-BM
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 1.75 50 99.8 0.076 10.3 9.5 16945 16945 -3 20.5
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 1.75 1.79 100 0.522 4.8 9.8 1105
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.75 29.66 16822 16822 854 99.29 0.176 0.176 0.175 0.1731 0.197 0.1944 RANDOM 23.855
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] 0.93 0.47 0.93 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.276 r_dihedral_angle_4_deg 27.59 r_dihedral_angle_3_deg 12.71 r_dihedral_angle_1_deg 6.167 r_scangle_it 3.804 r_scbond_it 2.305 r_mcangle_it 1.389 r_angle_refined_deg 1.378 r_mcbond_it 0.733 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.276 r_dihedral_angle_4_deg 27.59 r_dihedral_angle_3_deg 12.71 r_dihedral_angle_1_deg 6.167 r_scangle_it 3.804 r_scbond_it 2.305 r_mcangle_it 1.389 r_angle_refined_deg 1.378 r_mcbond_it 0.733 r_nbtor_refined 0.307 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.202 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.174 r_metal_ion_refined 0.138 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 695 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building