6YOZ

HiCel7B labelled with b-1,4-glucosyl cyclophellitol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A39 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829812 mg/mL protein in 20 mM pH 8 Tris buffer mixed 2:1 with 0.15 M sodium citrate, 0.8 M ammonium sulfate, 1 M lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
4.169.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102α = 90
b = 102β = 90
c = 278.85γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.8857.6211000.177114.216.2120246
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.911002.9780.51.116.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2A391.8857.621120246599599.9470.2030.20180.2362Random selection33.48
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]
0.6550.655-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.782
r_dihedral_angle_4_deg14.702
r_dihedral_angle_3_deg13.392
r_dihedral_angle_1_deg7.37
r_lrange_it6.464
r_lrange_other6.403
r_scangle_other5.517
r_scangle_it5.516
r_scbond_it3.938
r_scbond_other3.938
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.782
r_dihedral_angle_4_deg14.702
r_dihedral_angle_3_deg13.392
r_dihedral_angle_1_deg7.37
r_lrange_it6.464
r_lrange_other6.403
r_scangle_other5.517
r_scangle_it5.516
r_scbond_it3.938
r_scbond_other3.938
r_mcangle_other3.891
r_mcangle_it3.887
r_mcbond_it3.089
r_mcbond_other3.081
r_angle_other_deg2.457
r_angle_refined_deg1.786
r_symmetry_nbd_refined0.644
r_nbd_other0.262
r_nbd_refined0.226
r_symmetry_nbd_other0.216
r_symmetry_xyhbond_nbd_refined0.191
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.164
r_chiral_restr0.089
r_symmetry_nbtor_other0.083
r_bond_other_d0.036
r_symmetry_xyhbond_nbd_other0.031
r_bond_refined_d0.013
r_gen_planes_other0.013
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6100
Nucleic Acid Atoms
Solvent Atoms519
Heterogen Atoms184

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing