X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QGDPDB ENTRY 1QGD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.9298Crystallization trials revealed a reservoir mixture of 13.5-15 % PEG 6000 (w/v), 4% PEG 400 (v/v) and 2% glycerol (v/v) in 50 mM glycyl-glycine (pH 7.9) optimal for reproducible crystallization of single crystals. To induce crystallization 3 l protein solution (8-12 mg/ml, 0.6 mM ThDP, 5 mM CaCl2 in 50 mM glycyl-glycine (pH 7.9)) were mixed with 3 l of the reservoir solution at room temperature. , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.63α = 90
b = 85.33β = 125.69
c = 72.74γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV++Varimax HR2008-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.7520980.050.06314.782.557086559322.8-327.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.751.8596.20.3940.4942.82.48724

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1QGD1.75205593255928279698.410.1640.1640.1620.206RANDOM21.521
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]
-0.770.360.480.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.287
r_dihedral_angle_4_deg18.51
r_dihedral_angle_3_deg14.264
r_dihedral_angle_1_deg6.5
r_scangle_it4.686
r_scbond_it2.998
r_angle_refined_deg1.995
r_mcangle_it1.819
r_mcbond_it1.182
r_chiral_restr0.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.287
r_dihedral_angle_4_deg18.51
r_dihedral_angle_3_deg14.264
r_dihedral_angle_1_deg6.5
r_scangle_it4.686
r_scbond_it2.998
r_angle_refined_deg1.995
r_mcangle_it1.819
r_mcbond_it1.182
r_chiral_restr0.146
r_bond_refined_d0.024
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4715
Nucleic Acid Atoms
Solvent Atoms488
Heterogen Atoms68

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata reduction