☰ Navigation Tabs
Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-homocysteine 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 0.2M Na-K phosphate buffer, 6-10% PEG 6000, 0.25M ammonium sulfate. 0.5mM PLP
Crystal Properties Matthews coefficient Solvent content 2.79 55.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.405 α = 90 b = 152.882 β = 90 c = 80.595 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 2016-01-25 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 2 50 99.8 0.095 19.6 7.2 129275
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 2.03 100 0.614 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 20 118684 6310 96.69 0.18034 0.17901 0.1883 0.20557 0.2126 RANDOM 30.425
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] 0.09 -0.23 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.175 r_dihedral_angle_4_deg 16.354 r_dihedral_angle_3_deg 14.827 r_dihedral_angle_1_deg 6.285 r_long_range_B_refined 5.281 r_long_range_B_other 5.261 r_scangle_other 3.605 r_mcangle_other 2.864 r_mcangle_it 2.863 r_scbond_it 2.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.175 r_dihedral_angle_4_deg 16.354 r_dihedral_angle_3_deg 14.827 r_dihedral_angle_1_deg 6.285 r_long_range_B_refined 5.281 r_long_range_B_other 5.261 r_scangle_other 3.605 r_mcangle_other 2.864 r_mcangle_it 2.863 r_scbond_it 2.254 r_scbond_other 2.254 r_mcbond_it 1.837 r_mcbond_other 1.836 r_angle_refined_deg 1.523 r_angle_other_deg 0.981 r_chiral_restr 0.093 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 11849 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing