5K7P

MicroED structure of xylanase at 2.3 A resolution


ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DFB 

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.161α = 90
b = 59.752β = 90
c = 69.812γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (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
11.925.5566.60.4280.2452.73.63869910664
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9420.42.4772.2141.6348

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
ELECTRON CRYSTALLOGRAPHYFREE R-VALUE2.325.5491.34773436982.440.23130.22950.267
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_d10.687
f_angle_d0.496
f_chiral_restr0.043
f_plane_restr0.003
f_bond_d0.002

Software

Software
Software NamePurpose
PHENIXrefinement
Sample
Xylanase
Specimen Preparation
Sample Aggregation State3D ARRAY
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodCRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)2.3
Resolution MethodDIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type3D CRYSTAL
Space Group Name
Length a49.1
Length b59.02
Length c59.02
Angle Alpha90
Angle Beta90
Angle Gamma90
Map-Model Fitting and Refinement
Id1 (2DFB)
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeTVIPS TEMCAM-F416 (4k x 4k)
Electron Dose (electrons/Å**2)0.004
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeDIFFRACTION
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEM-Menu4.0.9.75
DIFFRACTION INDEXINGiMosflm/MOSFLM7.2.1
MODEL FITTINGMOLREP11.4.05
MODEL REFINEMENTPHENIX1.10_2155
MOLECULAR REPLACEMENTMOLREP11.4.05
SYMMETRY DETERMINATIONPOINTLESS1.10.21
CRYSTALLOGRAPHY MERGINGAIMLESS0.5.25
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE