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The crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021(T67A,Q69A) complex with NAD
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 2.0 M Ammonium sulfate
0.1 M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.08 60.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.6 α = 90 b = 131.6 β = 90 c = 115.886 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 2023-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
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 2.583 50 97.64 0.992 22.76 38.31 19107 38.31
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 2.583 2.68 0.938
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 2.583 43.524 18665 969 97.631 0.224 0.2215 0.2064 0.2716 0.2614 46.277
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] -0.201 -0.101 -0.201 0.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.59 r_dihedral_angle_6_deg 16.723 r_lrange_it 10.066 r_lrange_other 10.062 r_scangle_it 8.384 r_scangle_other 8.382 r_mcangle_it 7.182 r_mcangle_other 7.181 r_dihedral_angle_1_deg 6.434 r_scbond_it 5.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.59 r_dihedral_angle_6_deg 16.723 r_lrange_it 10.066 r_lrange_other 10.062 r_scangle_it 8.384 r_scangle_other 8.382 r_mcangle_it 7.182 r_mcangle_other 7.181 r_dihedral_angle_1_deg 6.434 r_scbond_it 5.872 r_scbond_other 5.871 r_dihedral_angle_2_deg 5.747 r_mcbond_it 5.043 r_mcbond_other 5.041 r_angle_refined_deg 1.487 r_angle_other_deg 0.73 r_dihedral_angle_other_2_deg 0.339 r_symmetry_nbd_other 0.232 r_nbd_refined 0.214 r_nbd_other 0.207 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_other 0.118 r_symmetry_nbd_refined 0.101 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.067 r_bond_refined_d 0.01 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 3300 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 49
Software Software Software Name Purpose HKL-3000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing