7F1P

Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant ligand-free form.


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
2.7855.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.137α = 90
b = 153.01β = 90
c = 80.792γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

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
12.45088.80.08514.9567753
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)
12.42.4473.80.771.53.9

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 REPLACEMENTTHROUGHOUT2O7C2.419.9557245308579.920.185860.183570.22738RANDOM45.169
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]
0.01-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.505
r_dihedral_angle_4_deg15.723
r_dihedral_angle_3_deg14.956
r_long_range_B_refined6.658
r_long_range_B_other6.657
r_dihedral_angle_1_deg6.178
r_scangle_other3.954
r_mcangle_it3.884
r_mcangle_other3.884
r_scbond_it2.355
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.505
r_dihedral_angle_4_deg15.723
r_dihedral_angle_3_deg14.956
r_long_range_B_refined6.658
r_long_range_B_other6.657
r_dihedral_angle_1_deg6.178
r_scangle_other3.954
r_mcangle_it3.884
r_mcangle_other3.884
r_scbond_it2.355
r_scbond_other2.354
r_mcbond_it2.305
r_mcbond_other2.305
r_angle_refined_deg1.373
r_angle_other_deg0.933
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms11879
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms

Software

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