6ZAG

Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and ACV after exposure to dioxygen for 500ms.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BLZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE8.52981.7 M Li2SO4, 0.1 M TRIS pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.1642.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.898α = 90
b = 75.879β = 90
c = 101.904γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX340-HS2018-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFXSLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection

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
11.420.2999.950.980.14835.087103.556489719.4464311825
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)
11.41.42499.970.0231.3110.40417.73

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 REPLACEMENTTHROUGHOUT1BLZ1.400120.28671.327664321198099.29450.16860.16820.181229.5166
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_d11.30992
f_angle_d0.6796
f_chiral_restr0.06713
f_plane_restr0.0043
f_bond_d0.00375
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2592
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms35

Software

Software
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction
PHASERphasing
cxi.mergedata scaling