5X2W

Crystal structure of Pseudomonas putida methionine gamma-lyase wild type 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 DROP2930.2 M Na-K phosphate buffer, 6-10 % PEG 6000, 0.25 M ammonium sulfate. 0.5 mM PLP
Crystal Properties
Matthews coefficientSolvent content
2.7855.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.635α = 90
b = 152.311β = 90
c = 80.487γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2016-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.748.999.80.1698.87.253025
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)
12.72.81000.4357.3

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 REPLACEMENTTHROUGHOUT2O7C2.72050074268099.490.197970.19540.24635RANDOM34.138
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]
-0.2-0.140.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.583
r_dihedral_angle_3_deg15.219
r_dihedral_angle_4_deg14.524
r_dihedral_angle_1_deg6.391
r_long_range_B_refined4.926
r_long_range_B_other4.925
r_mcangle_it2.737
r_mcangle_other2.735
r_scangle_other2.243
r_mcbond_it1.546
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.583
r_dihedral_angle_3_deg15.219
r_dihedral_angle_4_deg14.524
r_dihedral_angle_1_deg6.391
r_long_range_B_refined4.926
r_long_range_B_other4.925
r_mcangle_it2.737
r_mcangle_other2.735
r_scangle_other2.243
r_mcbond_it1.546
r_mcbond_other1.542
r_angle_refined_deg1.324
r_scbond_it1.257
r_scbond_other1.257
r_angle_other_deg0.936
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.005
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11849
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing