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The crystal structure of the prephenate dehydratase (PDT) from Staphylococcus aureus subsp. aureus Mu50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 289 0.1M Sodium citrate, 3M Sodium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.39 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.859 α = 90 b = 87.406 β = 90 c = 107.744 γ = 90
Symmetry Space Group P 21 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 315 mirror 2006-07-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929, 0.97942 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 2.3 45.88 98.4 0.068 56.5 11.1 25930 25930
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 2.35 97.8 0.439 5.5 10.5 1672
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 2.3 45.88 24569 24569 1320 98.14 0.22734 0.22734 0.22488 0.2223 0.2761 0.2732 RANDOM 63.484
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] 0.05 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.02 r_dihedral_angle_3_deg 22.463 r_dihedral_angle_4_deg 20.809 r_dihedral_angle_1_deg 8.402 r_scangle_it 4.474 r_scbond_it 3.063 r_angle_refined_deg 2.114 r_mcangle_it 1.995 r_mcbond_it 1.124 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.02 r_dihedral_angle_3_deg 22.463 r_dihedral_angle_4_deg 20.809 r_dihedral_angle_1_deg 8.402 r_scangle_it 4.474 r_scbond_it 3.063 r_angle_refined_deg 2.114 r_mcangle_it 1.995 r_mcbond_it 1.124 r_nbtor_refined 0.321 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.244 r_symmetry_vdw_refined 0.219 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.175 r_metal_ion_refined 0.15 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 4042 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing HKL-3000 phasing