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Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-methionine intermediates
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 293 0.2 M Na-K phosphate buffer, 6-10 % PEG 6000, 0.25 M ammonium sulfate. 0.5 mM PLP
Crystal Properties Matthews coefficient Solvent content 2.78 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.635 α = 90 b = 152.311 β = 90 c = 80.487 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE RIGAKU RAXIS IV++ 2016-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 48.9 99.8 0.169 8.8 7.2 53025
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 100 0.435 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2O7C 2.7 20 50074 2680 99.49 0.19797 0.1954 0.1983 0.24635 0.2427 RANDOM 34.138
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] -0.2 -0.14 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.583 r_dihedral_angle_3_deg 15.219 r_dihedral_angle_4_deg 14.524 r_dihedral_angle_1_deg 6.391 r_long_range_B_refined 4.926 r_long_range_B_other 4.925 r_mcangle_it 2.737 r_mcangle_other 2.735 r_scangle_other 2.243 r_mcbond_it 1.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.583 r_dihedral_angle_3_deg 15.219 r_dihedral_angle_4_deg 14.524 r_dihedral_angle_1_deg 6.391 r_long_range_B_refined 4.926 r_long_range_B_other 4.925 r_mcangle_it 2.737 r_mcangle_other 2.735 r_scangle_other 2.243 r_mcbond_it 1.546 r_mcbond_other 1.542 r_angle_refined_deg 1.324 r_scbond_it 1.257 r_scbond_other 1.257 r_angle_other_deg 0.936 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11849 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling MOLREP phasing