X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BI8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62985 mg/mL protein, 85 mM ammonium acetate, 42 mM tri-sodium citrate, 12.3% PEG 4000, 7.5% glycerol, 15 mM L-cysteine, 5 mM UDP-Glc, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1861.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.951α = 90
b = 93.951β = 90
c = 130.259γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmrhodium coated toroidal mirror2006-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B0.9002APS14-ID-B

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
12.455098.60.1114.8314.9417574116153.9
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)
2.452.54970.3664.24.94042

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 REPLACEMENTTHROUGHOUT2BI82.45304151040988206498.740.1940.1940.1920.238RANDOM45.792
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]
-1.79-1.793.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.225
r_dihedral_angle_4_deg19.512
r_dihedral_angle_3_deg16.612
r_dihedral_angle_1_deg6.663
r_scangle_it3.974
r_scbond_it2.857
r_angle_refined_deg1.712
r_mcangle_it1.698
r_mcbond_it1.466
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.225
r_dihedral_angle_4_deg19.512
r_dihedral_angle_3_deg16.612
r_dihedral_angle_1_deg6.663
r_scangle_it3.974
r_scbond_it2.857
r_angle_refined_deg1.712
r_mcangle_it1.698
r_mcbond_it1.466
r_nbtor_refined0.322
r_nbd_refined0.225
r_symmetry_vdw_refined0.18
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.158
r_chiral_restr0.117
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6238
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms163

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing