8VPW

Pseudomonas fluorescens G150T isocyanide hydratase at 298 K XFEL data, free enzyme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6NI4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE8.829815.5% PEG 3350, 125 MM MGCL2, AND 62 MM TRIS-HCL PH 8.8
Crystal Properties
Matthews coefficientSolvent content
2.2545.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.129α = 90
b = 59.853β = 115.887
c = 56.144γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX340-HS2021-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.033SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1coMESHinjection
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
16HPLCcrystallization buffer
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
14030912
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
119135

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
11.32299.970.9860.133554.115280313.28
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)
11.31.321000.4280.6251.3216.43

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 DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE1.3221.3452778199799.950.12890.1280.15218.1
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_d12.0736
f_angle_d0.8752
f_chiral_restr0.0786
f_plane_restr0.0082
f_bond_d0.0072
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1673
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms1

Software

Software
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction
cctbx.xfel.mergedata scaling
PHENIXphasing