X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FYQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2988% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A
Crystal Properties
Matthews coefficientSolvent content
3.1260.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.82α = 90
b = 153.82β = 90
c = 322.12γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDMAR CCD 165 mm2013-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim 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
13.55099.60.080.9910.94.155989
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.699.80.330.682.7

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-VALUE4FYQ3.50549.7951.3455987199199.640.24520.24440.266896.7655
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_d12.818
f_angle_d0.701
f_chiral_restr0.048
f_plane_restr0.007
f_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23307
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms353

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing