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Crystal structure of highly stable methionine gamma-lyase from Thermobrachium celere in complex with PLP and norleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Well solution: 26% PEG 400 and 0.1M MgCl2 in 1M MES pH 6.5
Cryoprotection: 30% PEG 400
Protein: 13.5 mg/ml in 50 mM HEPES pH 7.5, 100 mM NaCl,
1 mM PLP with 5 mM norleucin
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.426 α = 90 b = 86.426 β = 90 c = 862.41 γ = 120
Symmetry Space Group P 61 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 EIGER X 16M Kirkpatrick-Baez pair of bi-morph mirrors 2022-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
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 2.61 143.74 94.7 0.231 0.235 0.038 0.998 14.8 37.9 39975
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 2.61 2.9 74.4 2.982 3.023 0.496 0.623 1.6 36.4
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 2.607 37.84 39943 1998 65.7 0.2507 0.2498 0.2332 0.2678 0.2454 RANDOM 84.4
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] -1.4075 -1.4075 2.815
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.46 t_omega_torsion 2.33 t_angle_deg 0.9 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_nbd t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12263 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 100
Software Software Software Name Purpose BUSTER refinement Coot model building PHASER phasing XDS data reduction STARANISO data scaling Aimless data scaling autoPROC data processing