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The crystal structure of aspartate aminotransferases Lpg0070 from Legionella pneumophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other Aminotransferase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.1 M Ammonium sulfate
0.05 M Magnesium sulfate heptahydrate
0.1 M Sodium citrate 5.5
22.5 % v/v PEG Smear Medium
Crystal Properties Matthews coefficient Solvent content 2.68 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.425 α = 90 b = 105.425 β = 90 c = 165.471 γ = 90
Symmetry Space Group I 41 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 PIXEL DECTRIS PILATUS3 6M 2023-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.978 SSRF BL18U1
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 1.7 50 99 0.135 0.138 0.028 0.996 6.2 24.1 51188 23.29
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 1.7 1.76 90.7 1.373 1.411 0.311 0.707 19.2
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 48.92 50925 2584 99.045 0.156 0.1554 0.1717 0.1919 23.945
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] -0.016 -0.016 0.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.807 r_dihedral_angle_6_deg 17.997 r_dihedral_angle_3_deg 14.93 r_lrange_it 7.891 r_lrange_other 7.627 r_scangle_it 6.651 r_scangle_other 6.649 r_dihedral_angle_1_deg 5.862 r_scbond_other 4.513 r_scbond_it 4.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.807 r_dihedral_angle_6_deg 17.997 r_dihedral_angle_3_deg 14.93 r_lrange_it 7.891 r_lrange_other 7.627 r_scangle_it 6.651 r_scangle_other 6.649 r_dihedral_angle_1_deg 5.862 r_scbond_other 4.513 r_scbond_it 4.509 r_mcangle_it 3.819 r_mcangle_other 3.818 r_mcbond_it 2.763 r_mcbond_other 2.763 r_angle_refined_deg 1.426 r_angle_other_deg 0.705 r_nbd_other 0.313 r_nbd_refined 0.215 r_symmetry_nbd_other 0.208 r_symmetry_nbd_refined 0.201 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.175 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3004 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing