6ZAQ

Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and IPN after dioxygen exposure


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
2.1642.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.991α = 90
b = 75.552β = 90
c = 102.348γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMPCCD2017-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL21.137470SACLABL2

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1gel extruderinjection

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
11.642.371000.9860.12843.74172.064379020.6455892797
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6281000.5192.806

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 REPLACEMENTFREE R-VALUE1BLZ1.642.371.3643758199999.920.1770.1760.20631.19
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_d11.554
f_angle_d1.155
f_chiral_restr0.069
f_bond_d0.013
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2571
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms30

Software

Software
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing