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Crystal structure of methionine gamma-lyase from Fusobacterium nucleatum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 41% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.2M Ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.947 α = 90 b = 99.915 β = 90 c = 138.297 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2015-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.19 43.06 99.7 0.06 0.064 0.017 26.3 13.5 145156
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.22 96.8 0.25 0.285 0.097 6.7 8.3
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 2RFV 1.19 37.78 137866 7273 99.62 0.15243 0.15198 0.1515 0.16101 0.1608 RANDOM 10.703
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] 0.53 -0.03 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.642 r_dihedral_angle_4_deg 18.087 r_dihedral_angle_3_deg 11.438 r_dihedral_angle_1_deg 6.044 r_long_range_B_refined 3.098 r_long_range_B_other 2.922 r_scangle_other 1.497 r_angle_refined_deg 1.419 r_mcangle_other 1.069 r_mcangle_it 1.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.642 r_dihedral_angle_4_deg 18.087 r_dihedral_angle_3_deg 11.438 r_dihedral_angle_1_deg 6.044 r_long_range_B_refined 3.098 r_long_range_B_other 2.922 r_scangle_other 1.497 r_angle_refined_deg 1.419 r_mcangle_other 1.069 r_mcangle_it 1.068 r_scbond_it 0.932 r_scbond_other 0.931 r_angle_other_deg 0.908 r_mcbond_it 0.638 r_mcbond_other 0.637 r_chiral_restr 0.083 r_bond_refined_d 0.008 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 3022 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DIALS data reduction SCALA data scaling MOLREP phasing