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The crystal structure of methionine gamma-lyase from Citrobacter freundii in complex with L-cycloserine pyridoxal-5'-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RFV PDB ENTRY 2RFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 303 5% PEG2000 MME, 50 mM Tris-HCl, 0.2 mM PLP, 0.25% DTT, pH 8.5, soaked in 50 mM L-cycloserine for 7 minutes, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.27 α = 90 b = 122.89 β = 90 c = 126.61 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 100 IMAGE PLATE MAR scanner 345 mm plate 2005-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.843 EMBL/DESY, HAMBURG BW7B
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 1.6 15 94.5 0.048 17.28 4.5 55080 55080 26.8
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 1.6 1.65 94.3 0.396 3.6 3.9 4606
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2RFV 1.6 15 53896 53896 2893 97.48 0.142 0.142 0.139 0.1397 0.197 0.1985 RANDOM 28.688
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] 5.51 -2.81 -2.7
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 48.856 r_dihedral_angle_2_deg 37.696 r_sphericity_bonded 22.149 r_dihedral_angle_4_deg 18.427 r_dihedral_angle_3_deg 12.979 r_long_range_B_refined 7.555 r_scangle_other 7.364 r_rigid_bond_restr 7.26 r_long_range_B_other 7.248 r_scbond_it 6.376
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 48.856 r_dihedral_angle_2_deg 37.696 r_sphericity_bonded 22.149 r_dihedral_angle_4_deg 18.427 r_dihedral_angle_3_deg 12.979 r_long_range_B_refined 7.555 r_scangle_other 7.364 r_rigid_bond_restr 7.26 r_long_range_B_other 7.248 r_scbond_it 6.376 r_scbond_other 6.374 r_dihedral_angle_1_deg 6.35 r_mcangle_it 5.993 r_mcangle_other 5.96 r_mcbond_it 4.757 r_mcbond_other 4.738 r_angle_refined_deg 1.943 r_angle_other_deg 1.014 r_chiral_restr 0.144 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2993 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 57
Software Software Software Name Purpose MAR345dtb data collection PHASES phasing REFMAC refinement PROCESS data reduction PROCESS data scaling