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Crystal structure of L. monocytogenes MenD with Mg2+ and ThDP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LQ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291.15 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1M MOPS/HEPES-Na pH7.5, 0.02M 1,6-hexanediol, 0.02M 1-butanol, 0.02M (RS)-1,2-propanediol, 0.02M 2-propanol, 0.02M 1,4-butanediol, 0.02M 1,3-propanediol, 5 mM MgCl2, 1 mM ThDP, 1 mM TCEP
Crystal Properties Matthews coefficient Solvent content 3.45 64.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.025 α = 90 b = 176.025 β = 90 c = 100.144 γ = 120
Symmetry Space Group P 64 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 110 PIXEL DECTRIS EIGER X 16M 2023-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953732 Australian Synchrotron MX2
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 2.61 47.57 100 0.994 14.6 54.5 28314 52.58
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 2.61 2.73 0.76
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.61 47.57 1.35 28278 1410 99.94 0.2009 0.1991 0.1989 0.2353 0.2352 55.77
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.356 f_angle_d 0.5276 f_chiral_restr 0.0428 f_plane_restr 0.0048 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4535 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing