X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VJO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293100 mM MES, 900 mM - 1100 mM Na/K-tartrate
Crystal Properties
Matthews coefficientSolvent content
3.3963.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.46α = 90
b = 146.46β = 90
c = 146.46γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.918840SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.546.311000.137128.3940.6518225-358.003
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)
12.52.571001.6472.76

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 REPLACEMENTTHROUGHOUT3vjo2.546.311731391299.980.19820.19610.2391RANDOM60.698
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.097
r_dihedral_angle_4_deg13.268
r_dihedral_angle_3_deg12.922
r_mcangle_it8.496
r_mcbond_it5.506
r_mcbond_other5.499
r_dihedral_angle_1_deg5.486
r_angle_other_deg2.753
r_angle_refined_deg1.775
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.097
r_dihedral_angle_4_deg13.268
r_dihedral_angle_3_deg12.922
r_mcangle_it8.496
r_mcbond_it5.506
r_mcbond_other5.499
r_dihedral_angle_1_deg5.486
r_angle_other_deg2.753
r_angle_refined_deg1.775
r_chiral_restr0.093
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.009
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2333
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing