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Crystal structure of tagatose 1,6-diphosphate aldolase from Staphylococcus aureus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 10 mM zinc sulfate, 100 mM MES pH 6.5, 12.5 % PEG550 MME, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.9 74.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.704 α = 90 b = 84.704 β = 90 c = 202.759 γ = 90
Symmetry Space Group P 43 21 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 ADSC QUANTUM 315r 2009-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931 APS 19-ID
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 1.9 50 99.9 0.09 54.7 12.1 59080 59016 -3 24
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 1.9 1.93 100 0.484 6.43 11.8 2889
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 50 58917 58917 2984 99.88 0.14935 0.14935 0.14821 0.17098 0.1985 RANDOM 19.146
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] -0.24 -0.24 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.368 r_dihedral_angle_3_deg 13.467 r_dihedral_angle_4_deg 12.959 r_dihedral_angle_1_deg 5.532 r_scangle_it 3.595 r_scbond_it 2.145 r_angle_refined_deg 1.224 r_mcangle_it 1.097 r_mcbond_it 0.59 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.368 r_dihedral_angle_3_deg 13.467 r_dihedral_angle_4_deg 12.959 r_dihedral_angle_1_deg 5.532 r_scangle_it 3.595 r_scbond_it 2.145 r_angle_refined_deg 1.224 r_mcangle_it 1.097 r_mcbond_it 0.59 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2569 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 36
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM model building RESOLVE model building Coot model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing