4W7V

Crystal structure of XacCel5A in complex with cellobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GZJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52910.1M sodium cacodylate, 0.2 M sodium acetate, 28% PEG8000, 5% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.2545.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.186α = 90
b = 81.756β = 90
c = 48.168γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.459LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.4348.1798.90.0620.07112.154.14109499-323.61
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.431.5294.20.7890.9341.66

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 REPLACEMENTTHROUGHOUT1GZJ1.4348.1754738283199.280.13390.13190.173RANDOM20.226
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]
-0.31-0.370.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.697
r_sphericity_free30.838
r_dihedral_angle_4_deg27.032
r_dihedral_angle_3_deg13.046
r_sphericity_bonded12.656
r_dihedral_angle_1_deg6.049
r_rigid_bond_restr3.137
r_mcangle_it2.712
r_mcbond_it2.089
r_mcbond_other2.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.697
r_sphericity_free30.838
r_dihedral_angle_4_deg27.032
r_dihedral_angle_3_deg13.046
r_sphericity_bonded12.656
r_dihedral_angle_1_deg6.049
r_rigid_bond_restr3.137
r_mcangle_it2.712
r_mcbond_it2.089
r_mcbond_other2.056
r_angle_refined_deg1.302
r_angle_other_deg0.799
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2447
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms46

Software

Software
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling