X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VTUPDB ENTRY 3VTU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62892.0M Ammonium sulfate, 0.05M Tri-sodium citrate, 0.1M Potassium sodium tartrate, 5% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.8556.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.17α = 90
b = 64.12β = 90
c = 149.77γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2011-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

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
12.5249.9297.50.12812.920055
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)
12.522.6695.90.70132828

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 3VTU2.5249.9218984102597.150.214790.211270.27953RANDOM36.628
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]
-0.31-2.713.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.435
r_dihedral_angle_4_deg21.844
r_dihedral_angle_3_deg20.753
r_dihedral_angle_1_deg7.186
r_scangle_it4.51
r_scbond_it2.629
r_angle_refined_deg1.9
r_mcangle_it1.843
r_mcbond_it0.965
r_chiral_restr0.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.435
r_dihedral_angle_4_deg21.844
r_dihedral_angle_3_deg20.753
r_dihedral_angle_1_deg7.186
r_scangle_it4.51
r_scbond_it2.629
r_angle_refined_deg1.9
r_mcangle_it1.843
r_mcbond_it0.965
r_chiral_restr0.129
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3102
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms20

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling