8OMC

Y345F/F347Y/Y389F 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 DROP2911:1 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
1.9737.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.852α = 90
b = 67.93β = 105.46
c = 74.483γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-05-30MSINGLE 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)Rrim I (All)Rpim I (All)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
11.558.261000.0780.0920.0490.99910.96.9110533
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.531.3361.5820.840.5586.9

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 REPLACEMENTTHROUGHOUT1.558.2610504254681000.16220.160780.18922RANDOM18.962
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]
0.280.12-1.20.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.43
r_dihedral_angle_3_deg13.115
r_dihedral_angle_1_deg6.991
r_long_range_B_refined5.408
r_long_range_B_other5.364
r_scangle_other4.396
r_scbond_other3.194
r_scbond_it3.193
r_mcangle_other2.915
r_mcangle_it2.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.43
r_dihedral_angle_3_deg13.115
r_dihedral_angle_1_deg6.991
r_long_range_B_refined5.408
r_long_range_B_other5.364
r_scangle_other4.396
r_scbond_other3.194
r_scbond_it3.193
r_mcangle_other2.915
r_mcangle_it2.914
r_mcbond_it2.239
r_mcbond_other2.237
r_angle_refined_deg2.005
r_angle_other_deg0.685
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.013
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5579
Nucleic Acid Atoms
Solvent Atoms648
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
Aimlessdata scaling
REFMACphasing