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Crystal structure of truncated (ACT domain removed) prephenate dehydrogenase tyrA from Bacillus anthracis in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6U60
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.2 ul of 6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 5 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #46 (20%w/v PEG 3350, 0.2M Li citrate ) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci).
Crystal Properties Matthews coefficient Solvent content 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.774 α = 90 b = 118.882 β = 92.39 c = 75.558 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 315r 2020-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97929 APS 19-BM
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 2.4 50 99.7 0.114 0.114 0.137 0.076 5.6 3.1 51186 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 98.2 0.866 0.866 1.053 0.591 0.481 2.9
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 FOURIER SYNTHESIS THROUGHOUT 6U60 2.4 49.12 42767 2131 88.15 0.1692 0.167 0.1706 0.2155 0.2131 RANDOM 46.649
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] -0.26 0.43 0.06 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_3_deg 15.742 r_dihedral_angle_4_deg 13.433 r_dihedral_angle_1_deg 6.055 r_angle_refined_deg 1.441 r_angle_other_deg 1.287 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_3_deg 15.742 r_dihedral_angle_4_deg 13.433 r_dihedral_angle_1_deg 6.055 r_angle_refined_deg 1.441 r_angle_other_deg 1.287 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9095 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 183
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing