X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529117.5% PEG3350 (w/v), 100mM MgAc, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1342.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.323α = 96.12
b = 60.033β = 96.36
c = 67.114γ = 109.51
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702009-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1Photon FactoryBL-17A

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
11.950950.06454857
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)
1.92950.2646789

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 REPLACEMENTTHROUGHOUT3ebj1.947.7852062279493.470.216170.212880.276RANDOM35.844
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]
3.52.721.90.291.55-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.39
r_dihedral_angle_4_deg22.127
r_dihedral_angle_3_deg19.264
r_dihedral_angle_1_deg6.799
r_scangle_it5.945
r_scbond_it3.798
r_mcangle_it2.349
r_angle_refined_deg2.033
r_mcbond_it1.323
r_chiral_restr0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.39
r_dihedral_angle_4_deg22.127
r_dihedral_angle_3_deg19.264
r_dihedral_angle_1_deg6.799
r_scangle_it5.945
r_scbond_it3.798
r_mcangle_it2.349
r_angle_refined_deg2.033
r_mcbond_it1.323
r_chiral_restr0.16
r_bond_refined_d0.023
r_gen_planes_refined0.009
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 Atoms5882
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms67

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling