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Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant 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 0.1 M NA-K PHOSPHATE BUFFER, pH 5.6-5.8, 6-9 % PEG 6000, 0.25 M AMMONIUM SULFATE. 0.5 MM PLP, 0.5%(v/v) 2-mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 2.78 55.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.907 α = 90 b = 152.557 β = 90 c = 80.9 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 CCD MARMOSAIC 300 mm CCD 2017-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.4 50 98.5 0.062 19.8 6 74230
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 2.4 2.44 93.5 0.732 2.3 4.8
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 2.4 19.93 63824 3464 89.91 0.18186 0.17981 0.1853 0.21938 0.2232 RANDOM 42.632
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.801 r_dihedral_angle_4_deg 15.26 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_1_deg 6.493 r_long_range_B_refined 5.838 r_long_range_B_other 5.838 r_scangle_other 3.713 r_mcangle_other 3.55 r_mcangle_it 3.549 r_scbond_it 2.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.801 r_dihedral_angle_4_deg 15.26 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_1_deg 6.493 r_long_range_B_refined 5.838 r_long_range_B_other 5.838 r_scangle_other 3.713 r_mcangle_other 3.55 r_mcangle_it 3.549 r_scbond_it 2.231 r_scbond_other 2.231 r_mcbond_it 2.158 r_mcbond_other 2.155 r_angle_refined_deg 1.459 r_angle_other_deg 0.996 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 11833 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing