X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TB7PDB ENTRY 3TB7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52771.6 M ammonium sulfate, 5% PEG3350, 0.446 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7254.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.41α = 90
b = 70.65β = 90.43
c = 194.44γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2009-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.541

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
12.85196.11699.60.0611.13.453918938964
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)
12.852.951000.33133.57

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 3TB72.8527.70736974195699.340.252660.250330.29604RANDOM51.923
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]
0.50.05-0.14-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.299
r_dihedral_angle_3_deg19.865
r_dihedral_angle_4_deg18.956
r_dihedral_angle_1_deg7.021
r_scangle_it3.761
r_scbond_it2.072
r_mcangle_it2.017
r_angle_refined_deg1.617
r_mcbond_it1.068
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.299
r_dihedral_angle_3_deg19.865
r_dihedral_angle_4_deg18.956
r_dihedral_angle_1_deg7.021
r_scangle_it3.761
r_scbond_it2.072
r_mcangle_it2.017
r_angle_refined_deg1.617
r_mcbond_it1.068
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.006
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 Atoms8832
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
CNSrefinement
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling