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The crystal structure of Legionella pneumophila adenosylhomocysteinase Lpg2021 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 3.01 59.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.467 α = 90 b = 130.467 β = 90 c = 115.523 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 1.921 42.805 99.45 0.981 56.33 38.4 1710554 38.7
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 1.921 1.99 0.802
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 1.921 42.705 44469 2193 99.595 0.21 0.2095 0.2057 0.2204 0.2256 40.573
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] -0.005 -0.003 -0.005 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.789 r_dihedral_angle_3_deg 16.789 r_lrange_it 7.387 r_lrange_other 7.387 r_dihedral_angle_1_deg 6.517 r_scangle_it 6.51 r_scangle_other 6.508 r_scbond_it 4.782 r_scbond_other 4.78 r_mcangle_it 4.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.789 r_dihedral_angle_3_deg 16.789 r_lrange_it 7.387 r_lrange_other 7.387 r_dihedral_angle_1_deg 6.517 r_scangle_it 6.51 r_scangle_other 6.508 r_scbond_it 4.782 r_scbond_other 4.78 r_mcangle_it 4.414 r_mcangle_other 4.414 r_dihedral_angle_2_deg 4.377 r_mcbond_it 3.797 r_mcbond_other 3.795 r_angle_refined_deg 1.404 r_angle_other_deg 0.684 r_dihedral_angle_other_2_deg 0.27 r_nbd_refined 0.212 r_symmetry_nbd_other 0.21 r_symmetry_xyhbond_nbd_refined 0.21 r_nbd_other 0.207 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.176 r_symmetry_nbd_refined 0.149 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.015 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 287 Heterogen Atoms 49
Software Software Software Name Purpose HKL-3000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing