X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DBN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop, vapor diffusion8.32779.6 % PEG 8000, 0.8M LiCl, 100 mM Tris pH 8.3, sitting drop, vapor diffusion, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.564.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.495α = 90
b = 111.495β = 90
c = 145.487γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray92CCDMARMOSAIC 300 mm CCD2010-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1APS23-ID-B

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
12.935099.80.1575.46.72030720267
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)
12.93398.50.8613.9960

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4DBN2.93352030720089103198.40.19650.19410.2417RANDOM79.5058
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]
-0.89-0.891.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.825
r_dihedral_angle_4_deg18.188
r_dihedral_angle_3_deg18.17
r_dihedral_angle_1_deg5.896
r_angle_refined_deg1.317
r_angle_other_deg0.734
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.825
r_dihedral_angle_4_deg18.188
r_dihedral_angle_3_deg18.17
r_dihedral_angle_1_deg5.896
r_angle_refined_deg1.317
r_angle_other_deg0.734
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4099
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms78

Software

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