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Structure of apo Staphylococcus aureus D-tagatose-6-phosphate kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F02
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 25% PEG3350, 0.2M sodium thiocyanate, frozen in paratone, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.952 α = 90 b = 96.94 β = 94.42 c = 94.485 γ = 90
Symmetry Space Group P 1 21 1
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 210 2007-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-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 2.3 15 90.1 0.078 15.5 2.7 146479 55270
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 2.3 2.38 93.5 0.158 5.4 2.6 5686
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 2F02 2.3 14.99 146479 55227 2729 90.09 0.218 0.215 0.2088 0.283 0.2722 RANDOM 42.88
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] 0.28 -0.85 -0.39 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.687 r_dihedral_angle_4_deg 17.98 r_dihedral_angle_3_deg 15.294 r_dihedral_angle_1_deg 5.942 r_scangle_it 1.954 r_scbond_it 1.228 r_angle_refined_deg 1.19 r_mcangle_it 0.77 r_mcbond_it 0.464 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.687 r_dihedral_angle_4_deg 17.98 r_dihedral_angle_3_deg 15.294 r_dihedral_angle_1_deg 5.942 r_scangle_it 1.954 r_scbond_it 1.228 r_angle_refined_deg 1.19 r_mcangle_it 0.77 r_mcbond_it 0.464 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.083 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9566 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction JDirector data collection HKL-2000 data reduction MOLREP phasing