8OLH

Y345F 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 15 MG/ML PROTEIN SOLUTION WITH A PRECIPITANT SOLUTION CONTAINING 20% PEG 6000, 100 MM HEPES PH 7.0
Crystal Properties
Matthews coefficientSolvent content
1.9336.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.022α = 90
b = 67.788β = 105.66
c = 73.024γ = 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)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
11.2370.3297.80.0930.1160.070.9968.24.8191400
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)
11.231.250.9441.2670.8360.3572.8

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 REPLACEMENTTHROUGHOUT1.2370.32181802953597.770.134440.133170.15875RANDOM12.368
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]
-0.640.37-1.271.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.44
r_dihedral_angle_2_deg10.86
r_dihedral_angle_1_deg6.786
r_rigid_bond_restr3.863
r_long_range_B_refined3.429
r_long_range_B_other2.657
r_angle_refined_deg1.748
r_scangle_other1.712
r_mcangle_it1.343
r_mcangle_other1.343
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.44
r_dihedral_angle_2_deg10.86
r_dihedral_angle_1_deg6.786
r_rigid_bond_restr3.863
r_long_range_B_refined3.429
r_long_range_B_other2.657
r_angle_refined_deg1.748
r_scangle_other1.712
r_mcangle_it1.343
r_mcangle_other1.343
r_scbond_other1.284
r_scbond_it1.283
r_mcbond_it0.973
r_mcbond_other0.972
r_angle_other_deg0.624
r_chiral_restr0.097
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.002
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 Atoms5599
Nucleic Acid Atoms
Solvent Atoms997
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data reduction
Aimlessdata scaling
REFMACphasing