6R9V

Crystal structure of Pediococcus acidilactici lactate oxidase A94G mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J6X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72951.1M Sodium Malonate, 0.1M Hepes pH 7.0, 0.5% Jeffamine ED-2003.
Crystal Properties
Matthews coefficientSolvent content
3.4564.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.53α = 90
b = 135.53β = 90
c = 124.86γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125010011.9813.239425
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.05

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 REPLACEMENTTHROUGHOUT2J6X245.9237453197299.960.153060.151860.17512RANDOM24.29
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]
-1.32-1.322.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.611
r_dihedral_angle_4_deg21.371
r_dihedral_angle_3_deg12.988
r_dihedral_angle_1_deg6.36
r_long_range_B_refined5.849
r_long_range_B_other5.848
r_scangle_other4.82
r_scbond_it3.131
r_scbond_other3.13
r_mcangle_other2.347
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.611
r_dihedral_angle_4_deg21.371
r_dihedral_angle_3_deg12.988
r_dihedral_angle_1_deg6.36
r_long_range_B_refined5.849
r_long_range_B_other5.848
r_scangle_other4.82
r_scbond_it3.131
r_scbond_other3.13
r_mcangle_other2.347
r_mcangle_it2.346
r_mcbond_it1.626
r_mcbond_other1.623
r_angle_refined_deg1.544
r_angle_other_deg1.403
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
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 Atoms2786
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing