X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C2IProtein coordinates from PDB entry 3c2i. DNA coordinates from a currently unpublished model.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.529125% PEG3350, 0.1 M ammonium sulfate, 0.1 M tris
Crystal Properties
Matthews coefficientSolvent content
2.5752.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.753α = 68.15
b = 47.359β = 89.83
c = 54.623γ = 65.98
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.97945APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.339.8596.30.0680.0910.060.99210.12.214585
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3884.20.4490.6010.3970.7182.1

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTProtein coordinates from PDB entry 3c2i. DNA coordinates from a currently unpublished model.2.339.851379978596.30.23340.23060.285765.544
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]
-4.22-1.931.861.74-2.26-2.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.819
r_dihedral_angle_4_deg28.612
r_dihedral_angle_3_deg15.157
r_dihedral_angle_1_deg5.819
r_mcangle_it3.472
r_mcbond_other2.296
r_mcbond_it2.294
r_angle_refined_deg1.669
r_angle_other_deg1.316
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.819
r_dihedral_angle_4_deg28.612
r_dihedral_angle_3_deg15.157
r_dihedral_angle_1_deg5.819
r_mcangle_it3.472
r_mcbond_other2.296
r_mcbond_it2.294
r_angle_refined_deg1.669
r_angle_other_deg1.316
r_chiral_restr0.089
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1090
Nucleic Acid Atoms976
Solvent Atoms
Heterogen Atoms3

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing