5X2Z

Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-methionine intermediates


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O7C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2M Na-K phosphate buffer, 6-10% PEG 6000, 0.25M ammonium sulfate. 0.5mM PLP
Crystal Properties
Matthews coefficientSolvent content
2.7855.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.045α = 90
b = 153.29β = 90
c = 80.584γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2013-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9000SPring-8BL44XU

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
11.85098.50.10215.14.4176399
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)
11.81.8393.90.4792.45.8

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 REPLACEMENTTHROUGHOUT2O7C1.820156182824993.230.173980.172570.20053RANDOM26.913
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]
0.1-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.857
r_dihedral_angle_4_deg14.892
r_dihedral_angle_3_deg14.616
r_dihedral_angle_1_deg6.613
r_long_range_B_refined6.314
r_long_range_B_other6.194
r_scangle_other3.37
r_mcangle_it2.87
r_mcangle_other2.868
r_scbond_it2.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.857
r_dihedral_angle_4_deg14.892
r_dihedral_angle_3_deg14.616
r_dihedral_angle_1_deg6.613
r_long_range_B_refined6.314
r_long_range_B_other6.194
r_scangle_other3.37
r_mcangle_it2.87
r_mcangle_other2.868
r_scbond_it2.041
r_scbond_other2.041
r_mcbond_it1.747
r_mcbond_other1.743
r_angle_refined_deg1.501
r_angle_other_deg0.978
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11843
Nucleic Acid Atoms
Solvent Atoms902
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing