2XFD | pdb_00002xfd

vCBM60 in complex with cellobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherAPO-VCBM60

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
182.4 M SODIUM MALONATE, 10 MM CELLOTRIOSE, pH 8
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.61α = 90
b = 41.99β = 90
c = 80.08γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287CCDADSC CCDMIRRORS2009-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.1940.0498.40.0612.93.4306562
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)
11.191.2298.80.186.73.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTAPO-VCBM601.1940.0430656163098.350.118540.116990.130.147950.16RANDOM7.42
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]
0.14-0.03-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.039
r_sphericity_free14.526
r_dihedral_angle_4_deg9.114
r_dihedral_angle_3_deg8.342
r_dihedral_angle_1_deg6.932
r_sphericity_bonded5.408
r_scangle_it5.251
r_scbond_it3.957
r_mcangle_it2.925
r_mcbond_it2.107
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms816
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing