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Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant 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 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 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.792 α = 90 b = 153.378 β = 90 c = 80.678 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 RAYONIX MX300HE 2014-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 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 1.79 50 99.5 0.103 11 4.1 180464
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 1.8 1.83 99.3 0.451 2.8 3.7
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 1.79 20 166226 8763 97.01 0.17423 0.17269 0.1834 0.20374 0.2099 RANDOM 26.991
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] 0.05 -0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.609 r_dihedral_angle_4_deg 16.262 r_dihedral_angle_3_deg 14.687 r_dihedral_angle_1_deg 6.684 r_long_range_B_refined 6.296 r_long_range_B_other 6.278 r_scangle_other 3.752 r_mcangle_it 3.343 r_mcangle_other 3.343 r_scbond_it 2.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.609 r_dihedral_angle_4_deg 16.262 r_dihedral_angle_3_deg 14.687 r_dihedral_angle_1_deg 6.684 r_long_range_B_refined 6.296 r_long_range_B_other 6.278 r_scangle_other 3.752 r_mcangle_it 3.343 r_mcangle_other 3.343 r_scbond_it 2.324 r_scbond_other 2.323 r_mcbond_it 2.063 r_mcbond_other 2.063 r_angle_refined_deg 1.575 r_angle_other_deg 0.984 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 11766 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing