5M3Z

Crystal structure of Citrobacter freundii methionine gamma-lyase with C115H replacement in the complex with L-norleucine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RFV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293MGL 20mg/ml, PEG MME 2000 37.5%, 50 ml TrisHCl, 25mM DTT, 0.2 mM PLP
Crystal Properties
Matthews coefficientSolvent content
2.5852.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.513α = 90
b = 123.019β = 90
c = 127.577γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.95372ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.455099.10.0540.99914.94.478132
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4795.10.80.5694.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2RFV1.4588.5674318380698.910.130330.128320.16934RANDOM26.214
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]
0.210.71-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.801
r_sphericity_free29.771
r_sphericity_bonded20.356
r_dihedral_angle_4_deg16.755
r_dihedral_angle_3_deg13.3
r_scangle_other6.997
r_long_range_B_refined6.451
r_long_range_B_other6.375
r_dihedral_angle_1_deg6.327
r_rigid_bond_restr6.045
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.801
r_sphericity_free29.771
r_sphericity_bonded20.356
r_dihedral_angle_4_deg16.755
r_dihedral_angle_3_deg13.3
r_scangle_other6.997
r_long_range_B_refined6.451
r_long_range_B_other6.375
r_dihedral_angle_1_deg6.327
r_rigid_bond_restr6.045
r_scbond_it5.78
r_scbond_other5.779
r_mcangle_other4.97
r_mcangle_it4.966
r_mcbond_it4.298
r_mcbond_other4.248
r_angle_refined_deg1.833
r_angle_other_deg1.255
r_chiral_restr0.13
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.004
r_gen_planes_other0.002
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 Atoms2992
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing