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Crystal structure of Pseudomonas putida methionine gamma-lyase wild type without sulfate ion
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 7.2 293 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 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.219 α = 90 b = 153.535 β = 90 c = 80.579 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++ 2014-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2.4 48.75 97.9 0.157 7 3.7 75515
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 2.48 91.2 0.388 3.4
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 30 70404 3732 98.04 0.21907 0.21604 0.2215 0.2756 0.2764 RANDOM 29.443
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] 1.81 -1.06 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.088 r_dihedral_angle_4_deg 17.242 r_dihedral_angle_3_deg 16.625 r_dihedral_angle_1_deg 7.074 r_long_range_B_refined 6.563 r_long_range_B_other 6.563 r_mcangle_it 3.613 r_mcangle_other 3.613 r_scangle_other 3.077 r_mcbond_it 2.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.088 r_dihedral_angle_4_deg 17.242 r_dihedral_angle_3_deg 16.625 r_dihedral_angle_1_deg 7.074 r_long_range_B_refined 6.563 r_long_range_B_other 6.563 r_mcangle_it 3.613 r_mcangle_other 3.613 r_scangle_other 3.077 r_mcbond_it 2.111 r_mcbond_other 2.11 r_scbond_it 1.852 r_scbond_other 1.851 r_angle_refined_deg 1.589 r_angle_other_deg 0.833 r_chiral_restr 0.129 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 11891 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling MOLREP phasing