6IG7

Crystal structure of thermolysin delivered in polyacrylamide using x-ray free electron laser


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DM9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES277.5Tris-HCl, NaCl
Crystal Properties
Matthews coefficientSolvent content
2.346.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.663α = 90
b = 92.663β = 90
c = 128.591γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray296CCDRAYONIX MX225-HSKB mirror2018-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERPAL-XFEL BEAMLINE NCI1.2792PAL-XFELNCI

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injectorinjection
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
1CMD (carrier matrix delivery) injector800100HPLCgaspolyacrylamide
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1203059.7
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
12221347865228304

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
11.8131.571000.990.14634.67663.83087833.17
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)
11.81.861000.610.84091.16471

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 REPLACEMENTTHROUGHOUT5DM91.840.1241.333086685599.960.17350.17270.2024
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_d11.913
f_angle_d1.004
f_chiral_restr0.056
f_bond_d0.011
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2450
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms5

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling