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Crystal structure of lysine biosynthetic amino acid carrier protein LysW from Thermus thermophilus conjugated with alpha-aminoadipate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 2.0M Ammonium sulfate, 0.1M Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.932 α = 90 b = 48.932 β = 90 c = 38.654 γ = 120
Symmetry Space Group P 32 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 95 CCD ADSC QUANTUM 210 2009-10-24 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.28105, 1.28323, 1.25720 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.2 50 97.2 0.065 58.563 10.8 17120 16643 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 100 0.232 11.8 20.5 1646
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 (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 1.2 21.19 17121 15766 852 97.24 0.14592 0.14542 0.159 0.15544 0.168 RANDOM 10.325
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] 0.02 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.792 r_dihedral_angle_3_deg 11.454 r_dihedral_angle_4_deg 9.335 r_dihedral_angle_1_deg 4.769 r_sphericity_free 3.52 r_scangle_it 3.172 r_scbond_it 2.034 r_sphericity_bonded 1.949 r_mcangle_it 1.541 r_angle_refined_deg 1.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.792 r_dihedral_angle_3_deg 11.454 r_dihedral_angle_4_deg 9.335 r_dihedral_angle_1_deg 4.769 r_sphericity_free 3.52 r_scangle_it 3.172 r_scbond_it 2.034 r_sphericity_bonded 1.949 r_mcangle_it 1.541 r_angle_refined_deg 1.507 r_mcbond_it 0.943 r_angle_other_deg 0.901 r_rigid_bond_restr 0.843 r_mcbond_other 0.322 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 402 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling