1Y4I
Crystal structure of Citrobacter Freundii L-methionine-lyase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GC0 | PDB entry 1GC0 |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
2.9 | 57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.35 | α = 90 |
b = 121.83 | β = 90 |
c = 127.16 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 0.979 | EMBL/DESY, HAMBURG | BW7A |
Data Collection
Overall | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | R-Free | 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 | 0.209 | 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 | |
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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 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3024 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MAR345 | data collection |
XDS | data scaling |
AMoRE | phasing |