8OLP

Y345F/F347Y Variant of Dye Type Peroxidase Aa (DtpAa) from Streptomyces lividans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6TB8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72911:1 RATIO OF A 15 MG/ML PROTEIN SOLUTION WITH A PRECIPITANT SOLUTION CONTAINING 20% PEG 6000, 100 MM HEPES PH 7.0
Crystal Properties
Matthews coefficientSolvent content
1.9135.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.037α = 90
b = 68.127β = 105.42
c = 73.046γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.98DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.2770.42990.0660.99995174917
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.271.29831.5190.3390.63.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.2770.42166396848298.990.153720.151690.19253RANDOM16.731
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]
1.20.32-2.320.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.951
r_dihedral_angle_2_deg11.315
r_dihedral_angle_1_deg6.899
r_rigid_bond_restr5.13
r_long_range_B_refined3.399
r_long_range_B_other3.158
r_scangle_other2.654
r_scbond_it2.084
r_scbond_other2.084
r_mcangle_it1.966
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.951
r_dihedral_angle_2_deg11.315
r_dihedral_angle_1_deg6.899
r_rigid_bond_restr5.13
r_long_range_B_refined3.399
r_long_range_B_other3.158
r_scangle_other2.654
r_scbond_it2.084
r_scbond_other2.084
r_mcangle_it1.966
r_mcangle_other1.966
r_angle_refined_deg1.842
r_mcbond_it1.572
r_mcbond_other1.564
r_angle_other_deg0.655
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.005
r_bond_other_d0.001
r_dihedral_angle_4_deg
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5582
Nucleic Acid Atoms
Solvent Atoms689
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing