5X30

Crystal structure of Pseudomonas putida methionine gamma-lyase C116H 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 DROP2930.2M Na-K phosphate buffer, 6-10% PEG 6000, 0.25M ammonium sulfate. 0.5mM PLP
Crystal Properties
Matthews coefficientSolvent content
2.7755.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.753α = 90
b = 152.971β = 90
c = 80.586γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2014-02-04MSINGLE 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
11.75099.50.05118.54.7208507
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)
11.71.7397.90.4413.85.2

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 REPLACEMENTTHROUGHOUT2O7C1.7201968051041399.380.170930.169670.19508RANDOM29.41
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]
0.16-0.1-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.35
r_dihedral_angle_4_deg15.149
r_dihedral_angle_3_deg13.454
r_long_range_B_refined6.054
r_dihedral_angle_1_deg6.027
r_long_range_B_other5.862
r_scangle_other3.227
r_mcangle_it2.819
r_mcangle_other2.819
r_scbond_it1.968
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.35
r_dihedral_angle_4_deg15.149
r_dihedral_angle_3_deg13.454
r_long_range_B_refined6.054
r_dihedral_angle_1_deg6.027
r_long_range_B_other5.862
r_scangle_other3.227
r_mcangle_it2.819
r_mcangle_other2.819
r_scbond_it1.968
r_scbond_other1.962
r_mcbond_it1.69
r_mcbond_other1.69
r_angle_refined_deg1.417
r_angle_other_deg0.95
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.006
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 Atoms11900
Nucleic Acid Atoms
Solvent Atoms1021
Heterogen Atoms62

Software

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