8RGS

Serial synchrotron in plate room temperature structure of Dye Type Peroxidase Aa


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE72911:3 v/v ratio of 10 mg/ml protein in 20 mM sodium phosphate, 150 mM NaCl, pH 7.0 and a mother liquor solution (12% v/v PEG 3350, 100 mM HEPES pH 7.0)
Crystal Properties
Matthews coefficientSolvent content
2.243.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.474α = 90
b = 67.765β = 105.7
c = 74.733γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS EIGER2 X 4M2023-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE VMXi0.775DiamondVMXi

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1In Platefixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1Mitegen in situ-1 plate

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
11.7969.7799.750.990.12121.898.96582122
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)
11.791.8540.3150.978

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTFREE R-VALUE1.7969.771.3465657194699.750.18980.18860.228123.16
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_d15.2563
f_angle_d1.0531
f_chiral_restr0.0609
f_plane_restr0.0135
f_bond_d0.0087
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5503
Nucleic Acid Atoms
Solvent Atoms416
Heterogen Atoms86

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
xia2data reduction
xia2data scaling
PHENIXphasing