6Y0O

isopenicillin N synthase in complex with ACV and Fe under anaerobic environment using FT-SSX methods


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 pH8.5
Crystal Properties
Matthews coefficientSolvent content
2.1642.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.889α = 90
b = 75.797β = 90
c = 102.034γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS 6M2019-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96863DiamondI24

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed targetfixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1Anaerobicthin film mylar sandwich
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1

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
12.260.8597.710.9590.23515.02130.221688024.7373704023
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)
12.22.23899.750.1761.0041.47.96

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-VALUE1blz2.260.851.331674983397.720.2110.2090.24732.67
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_d8.47233818324
f_angle_d0.479095088091
f_chiral_restr0.0424090301173
f_plane_restr0.00289414633692
f_bond_d0.0024
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2584
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms35

Software

Software
Software NamePurpose
PHENIXrefinement
GDAdata collection
DIALSdata reduction
DIALSdata scaling
PHASERphasing