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The crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021 in ternary complex with NAD and adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other Q5ZTY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.5 M Ammonium sulfate
1.0 M Lithium sulfate
0.1 M Sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 3.07 59.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.82 α = 90 b = 130.82 β = 90 c = 117.118 γ = 120
Symmetry Space Group P 62 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 2023-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97861 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.649 50 100 0.102 0.103 0.017 0.999 50.3 38.6 71306
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 1.649 1.71 0.806
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Q5ZTY7 1.649 25.511 71071 3525 99.651 0.176 0.176 0.1828 0.1816 0.1922 25.143
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] -0.35 -0.175 -0.35 1.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.621 r_dihedral_angle_3_deg 15.107 r_lrange_it 6.566 r_dihedral_angle_1_deg 6.418 r_lrange_other 6.264 r_scangle_other 5.379 r_scangle_it 5.37 r_dihedral_angle_2_deg 4.314 r_scbond_other 3.676 r_scbond_it 3.669
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.621 r_dihedral_angle_3_deg 15.107 r_lrange_it 6.566 r_dihedral_angle_1_deg 6.418 r_lrange_other 6.264 r_scangle_other 5.379 r_scangle_it 5.37 r_dihedral_angle_2_deg 4.314 r_scbond_other 3.676 r_scbond_it 3.669 r_mcangle_it 3.022 r_mcangle_other 3.021 r_mcbond_it 2.236 r_mcbond_other 2.235 r_angle_refined_deg 1.405 r_angle_other_deg 0.681 r_dihedral_angle_other_2_deg 0.327 r_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.21 r_symmetry_nbd_other 0.207 r_nbd_other 0.189 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.171 r_symmetry_nbd_refined 0.111 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.068 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 3306 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing