6ZAJ

Room temperature XFEL Isopenicillin N synthase structure in complex with Fe, O2 and ACV after exposure to dioxygen for 3000ms.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE8.52981.7M Li2SO4, 0.1 M TRIS pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.1542.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.885α = 90
b = 75.639β = 90
c = 101.897γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX340-HS2018-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.30179SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1acoustic droplet tape driveinjection
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
1acoustic droplet tape drive

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
11.5321.1399.940.9750.1631.1690.714997222.1870954592
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)
11.531.5561000.1021.1130.67922.48

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 REPLACEMENTTHROUGHOUT1BLZ1.530121.12831.331749646199999.91950.17880.1780.198132.7271
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_d9.23386
f_angle_d0.93152
f_chiral_restr0.05975
f_bond_d0.00907
f_plane_restr0.00664
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2581
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms29

Software

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