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Crystal structure of methionine gamma-lyase from Brevibacterium aurantiacum having disordered N-terminus and devoid of PLP cofactor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PG8 Crystal Structure of L-methionine alpha-, gamma-lyase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 Well solution: 0.1 M MES pH 6.5, 0.6 M NaCl, 18% PEG4000, PLP 2 mM,
Cryoprotection in glycerol 25%
Crystal Properties Matthews coefficient Solvent content 2.22 41.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.848 α = 90 b = 165.848 β = 90 c = 209.263 γ = 90
Symmetry Space Group P 41 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 EIGER X 16M Kirkpatrick-Baez pair of bi-morph mirrors 2018-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 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 3.237 129.978 95.7 0.1532 0.1572 0.0351 0.999 13.06 20.01 30990
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) 3.237 3.628 77.3 1.9151 1.9621 0.4233 0.742 1.9 21.21 1549
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.238 32.76 30928 1518 65.8 0.2487 0.2469 0.2843 0.2693 RANDOM 163.93
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] 0.6572 0.6572 -1.3144
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.03 t_omega_torsion 1.87 t_angle_deg 0.79 t_bond_d 0.006 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 18176 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling BUSTER refinement Coot model building PHASER phasing