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Crystal structure of methionine gamma-lyase (K209Q variant) from Brevibacterium aurantiacum in complex with PLP and alpha-ketobutyrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GJ9 Methionine gamma-lyase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 Well solution 0.1 M Tris-HCl, pH 8.5, 0.1 M Lithium sulfate, 32% PEG4000, 1 mM PLP, 20 mM Methionine,
Cryoprotection: 10% PEG400
Crystal Properties Matthews coefficient Solvent content 2.48 47.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.328 α = 90 b = 155.89 β = 90.24 c = 232.079 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 9M a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors 2023-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98399 SOLEIL PROXIMA 2
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 2.522 232.077 93.6 0.3218 0.3498 0.1356 0.98 5.9 6.32 214191
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) 2.522 2.82 61.6 1.2192 1.3263 0.5162 0.44 1.63 6.27 10710
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.522 232.08 214191 10624 67.2 0.2581 0.2577 0.2474 0.2652 0.2558 RANDOM 59.77
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] 1.2175 2.9363 -3.5211 2.3036
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.47 t_omega_torsion 2.39 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 67475 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 652
Software Software Software Name Purpose MxCuBE data collection autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling Coot model building BUSTER refinement PHASER phasing