6NPQ

Pseudomonas fluorescens isocyanide hydratase at 298 K XFEL data


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NON 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE8.829831% PEG 3350, 250 mM MgCl2, 125 mM Tris-HCl, 2 mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.1743.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.879α = 90
b = 57.677β = 112.74
c = 68.778γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX340-HS2018-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.3SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1coMESHinjection
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
10.3
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
11059.5
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
121834

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
11.5520.1399.90.9620.19660.550.56007518.38
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)
11.551.5799.80.160.8626.3

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-VALUE3NON1.5520.131.3459628200299.930.16040.15950.186527.69
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_d12.8924
f_angle_d0.7765
f_chiral_restr0.0484
f_plane_restr0.0054
f_bond_d0.0046
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3368
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms

Software

Software
Software NamePurpose
cctbx.xfeldata reduction
cctbx.primedata scaling
PHENIXrefinement