6RHT

Structure of Pediococcus acidilactici putative lactate oxidase WT protein


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.151.1 M Sodium Malonate, 0.1 M Hepes pH 7.0, 0.5% Jeffamine ED-2003
Crystal Properties
Matthews coefficientSolvent content
3.5965.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.24α = 90
b = 135.24β = 90
c = 124.84γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.980ESRFMASSIF-1

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
11.995.6399.910.38.945969
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9281.895

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 REPLACEMENTTHROUGHOUT2J6X1.991.943658231199.90.191450.189930.22093RANDOM28.168
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]
-1.97-1.973.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_4_deg18.518
r_dihedral_angle_3_deg14.828
r_dihedral_angle_1_deg6.742
r_long_range_B_refined6.686
r_long_range_B_other6.653
r_scangle_other5.245
r_scbond_it3.435
r_scbond_other3.434
r_mcangle_other2.827
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_4_deg18.518
r_dihedral_angle_3_deg14.828
r_dihedral_angle_1_deg6.742
r_long_range_B_refined6.686
r_long_range_B_other6.653
r_scangle_other5.245
r_scbond_it3.435
r_scbond_other3.434
r_mcangle_other2.827
r_mcangle_it2.823
r_mcbond_it1.959
r_mcbond_other1.954
r_angle_refined_deg1.628
r_angle_other_deg1.37
r_chiral_restr0.074
r_bond_refined_d0.01
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 Atoms2787
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing