X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DUBpdb entry 1DUB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7289Wizard Full condition F6: 0.1 M Tris, 20% PEG 3000, 0.2 M CaCl2, crystal ID 208527F6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5251.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.853α = 90
b = 130.947β = 90
c = 102.218γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002009-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
11.893.697.50.08321.87.180982
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)
11.81.8681.90.5492.695.56722

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 1DUB1.85080847407397.260.1750.1740.192RANDOM22.9
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]
-0.280.85-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.494
r_dihedral_angle_4_deg15.198
r_dihedral_angle_3_deg11.553
r_dihedral_angle_1_deg5.028
r_scangle_it2.594
r_scbond_it1.498
r_angle_refined_deg1.056
r_mcangle_it0.903
r_angle_other_deg0.858
r_mcbond_it0.474
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.494
r_dihedral_angle_4_deg15.198
r_dihedral_angle_3_deg11.553
r_dihedral_angle_1_deg5.028
r_scangle_it2.594
r_scbond_it1.498
r_angle_refined_deg1.056
r_mcangle_it0.903
r_angle_other_deg0.858
r_mcbond_it0.474
r_mcbond_other0.09
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5637
Nucleic Acid Atoms
Solvent Atoms701
Heterogen Atoms27

Software

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