X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DWYPDB entry 3DWY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.150.2 M potassium thiocyanate, 0.1 M Bis-Tris, pH 5.5, 5% v/v ethylene glycol, 23% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3547.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.993α = 96.77
b = 42.002β = 109.7
c = 49.8γ = 99.39
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002012-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-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
11.055092.70.032132.2108956
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)
11.051.0987.80.3762.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3DWY1.0540.71103515544092.610.140.13890.1614RANDOM15.536
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]
0.140.22-0.230.370.27-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.593
r_sphericity_free23.645
r_dihedral_angle_4_deg18.922
r_dihedral_angle_3_deg12.259
r_sphericity_bonded11.453
r_rigid_bond_restr6.583
r_dihedral_angle_1_deg5.752
r_mcangle_it1.585
r_angle_refined_deg1.583
r_mcbond_it1.475
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.593
r_sphericity_free23.645
r_dihedral_angle_4_deg18.922
r_dihedral_angle_3_deg12.259
r_sphericity_bonded11.453
r_rigid_bond_restr6.583
r_dihedral_angle_1_deg5.752
r_mcangle_it1.585
r_angle_refined_deg1.583
r_mcbond_it1.475
r_mcbond_other1.387
r_angle_other_deg0.762
r_chiral_restr0.097
r_gen_planes_refined0.017
r_bond_refined_d0.01
r_gen_planes_other0.003
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1933
Nucleic Acid Atoms
Solvent Atoms385
Heterogen Atoms57

Software

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