7F1V

Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-homocysteine intermediates


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M NA-K PHOSPHATE BUFFER, pH 5.6-5.8, 6-9 % PEG 6000, 0.25 M AMMONIUM SULFATE. 0.5 MM PLP, 0.5%(v/v) 2-mercaptoethanol
Crystal Properties
Matthews coefficientSolvent content
2.7655.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.075α = 90
b = 152.299β = 90
c = 80.508γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2017-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-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
12.255097.50.0456.55.290099
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)
12.252.2995.40.5131.34.6

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 REPLACEMENTTHROUGHOUT2O7C2.2519.9775074396187.730.189780.187820.22658RANDOM38.614
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.595
r_dihedral_angle_4_deg14.961
r_dihedral_angle_3_deg14.919
r_dihedral_angle_1_deg6.39
r_long_range_B_refined5.687
r_long_range_B_other5.685
r_scangle_other3.449
r_mcangle_it3.346
r_mcangle_other3.346
r_scbond_it2.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.595
r_dihedral_angle_4_deg14.961
r_dihedral_angle_3_deg14.919
r_dihedral_angle_1_deg6.39
r_long_range_B_refined5.687
r_long_range_B_other5.685
r_scangle_other3.449
r_mcangle_it3.346
r_mcangle_other3.346
r_scbond_it2.063
r_scbond_other2.055
r_mcbond_it2.008
r_mcbond_other2.008
r_angle_refined_deg1.418
r_angle_other_deg0.979
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms11849
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms54

Software

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