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Crystal structure of prephenate dehydrogenase tyrA from Bacillus anthracis in complex with NAD and 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 6.2 289 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 20 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #81 (0.1 M Potassium/Sodium phosphate pH=6.2, 0.2M Sodium chloride, 20% w/v PEG 1000) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization the protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours
Crystal Properties Matthews coefficient Solvent content 2.22 44.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.85 α = 90 b = 81.003 β = 90 c = 83.597 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 MARMOSAIC 300 mm CCD Beryllium Lenses 2015-04-18 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) Rrim I (All) Rpim I (All) CC (Half) 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 2.1 50 99.8 0.075 0.08 0.027 0.999 9.1 8.5 42991 -3 24.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.3 1.302 1.411 0.534 0.612 1.6 6.7
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 2.1 36.48 38244 1975 93.44 0.1634 0.1605 0.1711 0.2203 0.2264 RANDOM 36.389
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] -0.59 -0.2 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.322 r_dihedral_angle_3_deg 15.419 r_dihedral_angle_4_deg 15.163 r_dihedral_angle_1_deg 6.281 r_angle_refined_deg 1.484 r_angle_other_deg 1.352 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.322 r_dihedral_angle_3_deg 15.419 r_dihedral_angle_4_deg 15.163 r_dihedral_angle_1_deg 6.281 r_angle_refined_deg 1.484 r_angle_other_deg 1.352 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5703 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing Coot model building HKL-3000 phasing SCALEPACK data scaling