7PN4

Evolved unspecific peroxygenase with A77L mutation in complex with naphthalene


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OXU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62911.6M sodium potassium phosphate pH 5.6, 5% MPD Soaking: 30 mM naphthalene, 2 hours, cryoprotected with 25% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.3347.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.957α = 90
b = 57.651β = 109.44
c = 60.628γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB MIRRORS2020-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979260ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.0548.11000.170.1850.0719.76.720970
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.111000.6680.7260.2813.86.7

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5OXU2.0548.119940101599.920.16980.16780.2094RANDOM24.626
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]
-1.190.82-1.791.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.607
r_dihedral_angle_4_deg18.062
r_dihedral_angle_3_deg12.676
r_dihedral_angle_1_deg6.826
r_angle_refined_deg1.373
r_angle_other_deg1.325
r_chiral_restr0.063
r_gen_planes_refined0.007
r_gen_planes_other0.007
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.607
r_dihedral_angle_4_deg18.062
r_dihedral_angle_3_deg12.676
r_dihedral_angle_1_deg6.826
r_angle_refined_deg1.373
r_angle_other_deg1.325
r_chiral_restr0.063
r_gen_planes_refined0.007
r_gen_planes_other0.007
r_bond_refined_d0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2517
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing