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)
TypeSourceAccession CodeDetails
experimental modelPDB 2RFVPDB ENTRY 2RFV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.53035% 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 coefficientSolvent content
2.5551.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.27α = 90
b = 122.89β = 90
c = 126.61γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2005-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.843EMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.61594.50.04817.284.5550805508026.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6594.30.3963.63.94606

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2RFV1.6155389653896289397.480.1420.1420.1390.197RANDOM28.688
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
KeyRefinement Restraint Deviation
r_sphericity_free48.856
r_dihedral_angle_2_deg37.696
r_sphericity_bonded22.149
r_dihedral_angle_4_deg18.427
r_dihedral_angle_3_deg12.979
r_long_range_B_refined7.555
r_scangle_other7.364
r_rigid_bond_restr7.26
r_long_range_B_other7.248
r_scbond_it6.376
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free48.856
r_dihedral_angle_2_deg37.696
r_sphericity_bonded22.149
r_dihedral_angle_4_deg18.427
r_dihedral_angle_3_deg12.979
r_long_range_B_refined7.555
r_scangle_other7.364
r_rigid_bond_restr7.26
r_long_range_B_other7.248
r_scbond_it6.376
r_scbond_other6.374
r_dihedral_angle_1_deg6.35
r_mcangle_it5.993
r_mcangle_other5.96
r_mcbond_it4.757
r_mcbond_other4.738
r_angle_refined_deg1.943
r_angle_other_deg1.014
r_chiral_restr0.144
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2993
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms57

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
REFMACrefinement
PROCESSdata reduction
PROCESSdata scaling