4OMA
The crystal structure of methionine gamma-lyase from Citrobacter freundii in complex with L-cycloserine pyridoxal-5'-phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2RFV | PDB ENTRY 2RFV |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
2.55 | 51.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.27 | α = 90 |
b = 122.89 | β = 90 |
c = 126.61 | 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 | 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 | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | 1.6 | 1.65 | 94.3 | 0.396 | 3.6 | 3.9 | 4606 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | 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 | 0.197 | 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 | |
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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 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2993 |
Nucleic Acid Atoms | |
Solvent Atoms | 266 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
PHASES | phasing |
REFMAC | refinement |
PROCESS | data reduction |
PROCESS | data scaling |