5X2Y

Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant without sulfate ion


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
2.7955.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.792α = 90
b = 153.378β = 90
c = 80.678γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2014-01-24MSINGLE 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
11.795099.50.103114.1180464
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)
11.81.8399.30.4512.83.7

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 REPLACEMENTTHROUGHOUT2O7C1.7920166226876397.010.174230.172690.20374RANDOM26.991
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]
0.05-0.01-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.609
r_dihedral_angle_4_deg16.262
r_dihedral_angle_3_deg14.687
r_dihedral_angle_1_deg6.684
r_long_range_B_refined6.296
r_long_range_B_other6.278
r_scangle_other3.752
r_mcangle_it3.343
r_mcangle_other3.343
r_scbond_it2.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.609
r_dihedral_angle_4_deg16.262
r_dihedral_angle_3_deg14.687
r_dihedral_angle_1_deg6.684
r_long_range_B_refined6.296
r_long_range_B_other6.278
r_scangle_other3.752
r_mcangle_it3.343
r_mcangle_other3.343
r_scbond_it2.324
r_scbond_other2.323
r_mcbond_it2.063
r_mcbond_other2.063
r_angle_refined_deg1.575
r_angle_other_deg0.984
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.007
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 Atoms11766
Nucleic Acid Atoms
Solvent Atoms696
Heterogen Atoms

Software

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