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Crystal structure of Citrobacter Freundii L-methionine-lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GC0 PDB entry 1GC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 303 35% MMEPEG 2000, 200mM ammonium sulphate, 50mM TrisHCl, 0.2mM PLP, 0.25% DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.35 α = 90 b = 121.83 β = 90 c = 127.16 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 110 CCD MARRESEARCH 2004-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.979 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.89 20 95.2 0.057 18.3 3.96 34696 34696 16
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 1.98 2 83.9 0.382 4.1 3.7 4712
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1GC0 1.9 18.66 2 34154 33874 1700 96.9 0.214 0.206 0.206 0.208 0.209 0.2115 RANDOM 32.4
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] 12.1 -6.1 -6
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 3.98 c_scbond_it 3.07 c_mcangle_it 2.37 c_improper_angle_d 2.08 c_angle_deg 1.6 c_mcbond_it 1.48 c_bond_d 0.022 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 3.98 c_scbond_it 3.07 c_mcangle_it 2.37 c_improper_angle_d 2.08 c_angle_deg 1.6 c_mcbond_it 1.48 c_bond_d 0.022 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3024 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 5
Software Software Software Name Purpose CNS refinement MAR345 data collection XDS data scaling AMoRE phasing