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Structure of the pyridoxal 5'-phosphate-dependent (PLP) threonine deaminase ilvA1 from Pseudomonas aeruginosa PAO1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.6 293 15% (w/v) PEG-6000, 0.1 M Bicine/sodium hydroxide
Crystal Properties Matthews coefficient Solvent content 3.27 62.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.062 α = 90 b = 114.062 β = 90 c = 191.45 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS PILATUS 6M 2019-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 50 100 0.031 25.2 10 64851
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 0.287
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 35.73 62420 1992 99.34 0.1735 0.17261 0.20174 0.2015 RANDOM 48.36
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] 0.09 0.05 0.09 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.783 r_dihedral_angle_2_deg 10.835 r_dihedral_angle_1_deg 6.754 r_long_range_B_refined 5.068 r_long_range_B_other 5.042 r_scangle_other 2.92 r_mcangle_it 2.37 r_mcangle_other 2.37 r_scbond_it 1.712 r_scbond_other 1.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.783 r_dihedral_angle_2_deg 10.835 r_dihedral_angle_1_deg 6.754 r_long_range_B_refined 5.068 r_long_range_B_other 5.042 r_scangle_other 2.92 r_mcangle_it 2.37 r_mcangle_other 2.37 r_scbond_it 1.712 r_scbond_other 1.712 r_mcbond_it 1.412 r_mcbond_other 1.412 r_angle_refined_deg 1.261 r_angle_other_deg 0.455 r_chiral_restr 0.059 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7754 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 21
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building REFMAC refinement