6I43

SFX Structure of Damage Free Ferric State of Dye Type Peroxidase Aa from Streptomyces lividans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MAPPDB 5MAP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE72911:1 ratio of a 6.5 mg/ml DtpAa protein solution with a precipitant solution containing 20% PEG 6000, 100 mM HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2745.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.72α = 90
b = 68.18β = 105.58
c = 74.62γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray301CCDMPCCD2017-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL21.24SACLABL2

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1Silicon nitride fixed targetfixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1Mother liquor
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
110301.6610.01

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8841.461000.9930.07229.638157351
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.911000.7220.5831.73212

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 REPLACEMENTTHROUGHOUTPDB 5MAP1.8835.4581.3557312285299.970.13360.13190.1665
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_d13.08
f_angle_d0.919
f_chiral_restr0.052
f_bond_d0.009
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5466
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms86

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing