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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 AF-Q5ZZE1-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M Sodium sulfate
20% w/v PEG 3350
10% v/v Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.16 α = 90 b = 201.02 β = 90 c = 151.49 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 16M 2023-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.987 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.14 75.86 99.9 0.991 8.4 12.3 55245 45.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.2 100 0.579 1.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.14 75.86 55179 2715 99.751 0.238 0.2357 0.2373 0.2816 0.2855 53.81
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] 4.673 -4 -0.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.931 r_dihedral_angle_6_deg 18.137 r_lrange_other 10.567 r_lrange_it 10.563 r_scangle_it 9.309 r_scangle_other 9.299 r_mcangle_it 7.203 r_mcangle_other 7.202 r_scbond_it 6.51 r_scbond_other 6.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.931 r_dihedral_angle_6_deg 18.137 r_lrange_other 10.567 r_lrange_it 10.563 r_scangle_it 9.309 r_scangle_other 9.299 r_mcangle_it 7.203 r_mcangle_other 7.202 r_scbond_it 6.51 r_scbond_other 6.494 r_dihedral_angle_1_deg 6.252 r_mcbond_it 5.386 r_mcbond_other 5.385 r_angle_refined_deg 1.496 r_angle_other_deg 0.741 r_dihedral_angle_2_deg 0.59 r_symmetry_nbd_other 0.233 r_nbd_other 0.219 r_nbd_refined 0.217 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.12 r_symmetry_nbd_refined 0.085 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.08 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6022 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing