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Crystal Structure of methylglyoxal synthase from Borrelia burgdorferi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-O51339-F1-model_v4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 Morpheus Fusion D7: 20% (v/v) Ethylene glycol; 10% (w/v) PEG 8000, 0.05M Tris (base); 0.05M BICINE pH 8.5, 0.01M Sodium fluoride, 0.01M Sodium bromide, 0.01M Sodium iodide, 0.2 M xylitol, 0.02 M D-{-)-fructose, 0.02 M D-sorbitol, 0.02 M myo-inositol, 0.02 M L-rhamnose monohydrate. BobuA.00692.a.A1.PB00123 at 15 mg/mL. plate 13451 well D7 drop1. Puck: PSL-0612, Cryo: direct.
Crystal Properties Matthews coefficient Solvent content 2.87 57.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.866 α = 90 b = 110.866 β = 90 c = 91.256 γ = 90
Symmetry Space Group P 43 21 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 EIGER2 XE 9M 2023-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.5 49.58 100 0.15 0.153 0.032 1 17 23.8 20304
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 100 2.994 3.055 0.601 0.771 25.5
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 2.5 34.25 1.33 20222 988 99.87 0.1998 0.198 0.2009 0.2357 0.2366
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 13.321 f_angle_d 0.556 f_chiral_restr 0.045 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2948 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing