6I8E

Dye type peroxidase Aa from Streptomyces lividans: 65.6 kGy structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I43 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE82937 mg/ml protein mixed with 17% PEG 1500 and 67 mM MIB buffer (comprising imidazole, malonate and boric acid)
Crystal Properties
Matthews coefficientSolvent content
2.2846.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.961α = 90
b = 68.298β = 105.69
c = 74.787γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 6M2018-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1Silicon nitride chipsfixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1suction loaded onto chipSilicon nitride chipsaluminium holdergeobrickMother liquor
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)R Split (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
11.7844.71000.7660.950.182.9628.467896
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.811000.7480.6720.5160.7810.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6I431.7844.6121.3667896199899.990.16750.16620.2114
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d7.926
f_angle_d0.82
f_chiral_restr0.048
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5542
Nucleic Acid Atoms
Solvent Atoms458
Heterogen Atoms86

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
cctbx.primedata scaling
MOLREPphasing