5FW4

Structure of Thermobifida fusca DyP-type Peroxidase and Activity towards Kraft Lignin and Lignin Model Compounds


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GS1PDB ENTRY 4GS1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.520% PEG 3350, 100 MM BIS TRIS PROPANE PH 8.5, 0.2 M SODIUM BROMIDE
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.36α = 90
b = 110.21β = 90
c = 46.73γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I24DiamondI24

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
11.84299.80.0714.75.169391-323.425
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)
11.81.999.80.443.25

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4GS11.841.2166586280599.70.206050.204260.24927RANDOM31.354
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]
-2.235.22-2.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.606
r_dihedral_angle_4_deg17.482
r_dihedral_angle_3_deg14.477
r_dihedral_angle_1_deg6.486
r_angle_refined_deg1.641
r_angle_other_deg0.843
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.606
r_dihedral_angle_4_deg17.482
r_dihedral_angle_3_deg14.477
r_dihedral_angle_1_deg6.486
r_angle_refined_deg1.641
r_angle_other_deg0.843
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.008
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5586
Nucleic Acid Atoms
Solvent Atoms412
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing