X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5L7R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M BisTRis pH 6.0-7.0 17 % PEG MME2k 10 mM GalNAc
Crystal Properties
Matthews coefficientSolvent content
2.345.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.345α = 90
b = 142.207β = 90
c = 145.806γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9184DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.1651000.1040.999126.568163
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.151001.531.26.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5l7r2.16468085328399.910.19430.19270.2267RANDOM52.2065
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]
-2.671.081.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.897
r_dihedral_angle_3_deg16.537
r_dihedral_angle_4_deg15.698
r_dihedral_angle_1_deg6.866
r_angle_other_deg3.661
r_mcangle_it2.18
r_angle_refined_deg1.592
r_mcbond_it1.369
r_mcbond_other1.369
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.897
r_dihedral_angle_3_deg16.537
r_dihedral_angle_4_deg15.698
r_dihedral_angle_1_deg6.866
r_angle_other_deg3.661
r_mcangle_it2.18
r_angle_refined_deg1.592
r_mcbond_it1.369
r_mcbond_other1.369
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_other0.013
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9016
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing