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Crystal structure of prephenate dehydrogenase tyrA from Bacillus anthracis in complex with L-tyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GGG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2 ul of 19 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, and 10 mM BME were mixed with 0.2 ul of the MCSG Suite 1 condition #11 (0.1 M MES pH=6.5, 0.2 M Magnesium chloride, 10% w/v PEG 4000) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). His-tag was removed prior to crystallization.
Crystal Properties Matthews coefficient Solvent content 2.35 47.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.682 α = 90 b = 105.588 β = 90 c = 179.625 γ = 90
Symmetry Space Group P 21 21 21
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 Beryllium Lenses 2014-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.6 50 99.9 0.069 0.069 0.071 0.027 8.2 7.4 50884 -3 71.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 100 0.963 0.374 0.803 2.1 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3GGG 2.6 50 47834 2466 99.93 0.1913 0.1886 0.1892 0.2461 0.2407 RANDOM 76.618
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] -0.39 -1.19 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.506 r_dihedral_angle_3_deg 17.361 r_dihedral_angle_4_deg 15.182 r_dihedral_angle_1_deg 6.149 r_angle_refined_deg 1.732 r_angle_other_deg 1.581 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.506 r_dihedral_angle_3_deg 17.361 r_dihedral_angle_4_deg 15.182 r_dihedral_angle_1_deg 6.149 r_angle_refined_deg 1.732 r_angle_other_deg 1.581 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11332 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 52
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing HKL-3000 phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling