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The crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021(I255A,T287A) in ternary complex with NAD and adenosine
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 0.1 M Potassium thiocyanate, 30% w/v PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.98 58.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.657 α = 90 b = 130.657 β = 90 c = 113.834 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 2023-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97923 SSRF BL19U1
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 1.92 50 99.68 0.944 3.9 38.5 44078 28.04
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 1.922 1.991 0.856
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 1.922 37.945 43919 2145 99.685 0.206 0.2055 0.2088 0.2252 0.229 28.875
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] -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.627 r_dihedral_angle_3_deg 15.248 r_lrange_it 7.311 r_lrange_other 7.31 r_dihedral_angle_1_deg 6.483 r_scangle_it 6.15 r_scangle_other 6.149 r_scbond_it 4.481 r_scbond_other 4.479 r_dihedral_angle_2_deg 4.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.627 r_dihedral_angle_3_deg 15.248 r_lrange_it 7.311 r_lrange_other 7.31 r_dihedral_angle_1_deg 6.483 r_scangle_it 6.15 r_scangle_other 6.149 r_scbond_it 4.481 r_scbond_other 4.479 r_dihedral_angle_2_deg 4.343 r_mcangle_it 3.976 r_mcangle_other 3.976 r_mcbond_it 3.228 r_mcbond_other 3.228 r_angle_refined_deg 1.406 r_angle_other_deg 0.681 r_dihedral_angle_other_2_deg 0.268 r_nbd_refined 0.214 r_symmetry_nbd_other 0.212 r_nbd_other 0.202 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.179 r_xyhbond_nbd_refined 0.17 r_symmetry_nbd_refined 0.104 r_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.07 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 3301 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing