2QJE

Crystal structure of the complex of Bovine C-lobe with Amygdalin at 2.3A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DOJPDB entry 2DOJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M MES, PEG MONOMETHYLETHER, 0.1M ZNSO4, VAPOR DIFFUSION, HANGING DROP, pH 6.5, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.6453.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.368α = 90
b = 50.368β = 107.71
c = 65.969γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMAR scanner 345 mm plateGraphite2007-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.3500.10724.911643642.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.380.10724.91

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2DOJ2.339.316436800920.2230.2230.2230.227RANDOM37.3
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]
4.47-2.2-2.16-2.31
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.4
c_angle_deg1.8
c_mcangle_it1.74
c_improper_angle_d1.08
c_scbond_it1.06
c_mcbond_it0.97
c_bond_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2593
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms136

Software

Software
Software NamePurpose
CNSrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing