3GED

Fingerprint and Structural Analysis of a Apo SCOR enzyme from Clostridium thermocellum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YDEPDB entries 1YDE, 1VL8
experimental modelPDB 1VL8PDB entries 1YDE, 1VL8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
129825% (w/v) PEG 4000,100mM TAPs pH 9.0, 50mM sodium thiosulfate pentahydrate 1:1 cocktail to protein ratio (10mg/ml), hanging drop vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8657.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.287α = 90
b = 124.287β = 90
c = 162.608γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC Q3152006-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.979454SSRLBL11-1

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
11.41699.01597.70.06418.91268407-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.691.74

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB entries 1YDE, 1VL81.69849.6841.3368407344297.690.180.1790.20832.972
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]
-0.339-0.3390.677
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.848
f_angle_d1.327
f_chiral_restr0.094
f_bond_d0.011
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3758
Nucleic Acid Atoms
Solvent Atoms551
Heterogen Atoms29

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing