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
2.142.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.504α = 96.06
b = 60.211β = 96.49
c = 67.215γ = 109.66
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC 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
12.550980.082011219014
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)
2.52.60.303

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 REPLACEMENTTHROUGHOUT3EBJ2.5301802097173.760.242830.240310.2887RANDOM42.898
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]
-0.32-0.350.050.050.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.332
r_dihedral_angle_3_deg23.283
r_dihedral_angle_4_deg17.933
r_dihedral_angle_1_deg7.934
r_scangle_it3.262
r_scbond_it1.958
r_angle_refined_deg1.818
r_mcangle_it1.383
r_mcbond_it0.723
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.332
r_dihedral_angle_3_deg23.283
r_dihedral_angle_4_deg17.933
r_dihedral_angle_1_deg7.934
r_scangle_it3.262
r_scbond_it1.958
r_angle_refined_deg1.818
r_mcangle_it1.383
r_mcbond_it0.723
r_chiral_restr0.127
r_bond_refined_d0.019
r_gen_planes_refined0.007
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 Atoms5784
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms8

Software

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