☰ Navigation Tabs
Crystal structure of valine-pyruvate aminotransferase AvtA (NP_462565.1) from Salmonella typhimurium LT2 at 1.80 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 NANODROP, 40.0% Ethylene glycol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.94 58.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.28 α = 90 b = 92.28 β = 90 c = 227.33 γ = 120
Symmetry Space Group P 61 2 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 325 mm CCD Flat mirror (vertical focusing) 2008-11-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97874, 0.97828 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 29.285 99.8 0.066 14.25 10.2 53916 -3 28.602
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 98.2 0.943 1.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.8 29.28 53818 2733 99.83 0.17886 0.17797 0.1873 0.19577 0.2123 RANDOM 29.685
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] 0.1 0.05 0.1 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.893 r_dihedral_angle_4_deg 16.627 r_dihedral_angle_3_deg 10.367 r_scangle_it 6.383 r_scbond_it 4.478 r_dihedral_angle_1_deg 3.945 r_mcangle_it 2.677 r_mcbond_it 1.806 r_angle_refined_deg 1.589 r_angle_other_deg 1.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.893 r_dihedral_angle_4_deg 16.627 r_dihedral_angle_3_deg 10.367 r_scangle_it 6.383 r_scbond_it 4.478 r_dihedral_angle_1_deg 3.945 r_mcangle_it 2.677 r_mcbond_it 1.806 r_angle_refined_deg 1.589 r_angle_other_deg 1.018 r_mcbond_other 0.424 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.224 r_symmetry_vdw_other 0.202 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.183 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.176 r_nbtor_other 0.085 r_chiral_restr 0.076 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2976 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing