X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KG9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1829314% (w/v) PEG 4000, 200 mM CaCl2, 10% (v/v) glycerol, 2 mM DTT, 100 mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4850.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.379α = 90
b = 198.385β = 90
c = 146.764γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRRORS2007-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.7501000.1090.10918.17.435542
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)
12.72.81000.7926.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KG72.741.893527033290198099.160.215490.212540.2651RANDOM70.591
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]
-3.06-1.424.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.279
r_dihedral_angle_3_deg15.946
r_dihedral_angle_4_deg13.981
r_dihedral_angle_1_deg5.025
r_mcangle_it1.389
r_angle_refined_deg0.918
r_scangle_it0.885
r_mcbond_it0.809
r_scbond_it0.58
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.279
r_dihedral_angle_3_deg15.946
r_dihedral_angle_4_deg13.981
r_dihedral_angle_1_deg5.025
r_mcangle_it1.389
r_angle_refined_deg0.918
r_scangle_it0.885
r_mcbond_it0.809
r_scbond_it0.58
r_nbtor_refined0.299
r_symmetry_vdw_refined0.185
r_nbd_refined0.172
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.12
r_chiral_restr0.061
r_symmetry_metal_ion_refined0.056
r_metal_ion_refined0.051
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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 Atoms8802
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms5

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling