X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KT0PDB ENTRY 3KT0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.92770.1M HEPES, 2.2M (NH4)2SO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
5.05692975.676941

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 251.759α = 90
b = 251.759β = 90
c = 111.102γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2008-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
12.65096.30.05622.54.5118348
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)
2.62.6983.40.3442.310202

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 3KT02.648.94112240591896.080.215350.214210.23672RANDOM53.4
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]
-2.08-1.04-2.083.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.779
r_dihedral_angle_3_deg16.266
r_dihedral_angle_4_deg14.477
r_dihedral_angle_1_deg5.127
r_scangle_it4.919
r_rigid_bond_restr4.151
r_scbond_it3.888
r_mcangle_it2.938
r_mcbond_it2.342
r_sphericity_bonded1.522
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.779
r_dihedral_angle_3_deg16.266
r_dihedral_angle_4_deg14.477
r_dihedral_angle_1_deg5.127
r_scangle_it4.919
r_rigid_bond_restr4.151
r_scbond_it3.888
r_mcangle_it2.938
r_mcbond_it2.342
r_sphericity_bonded1.522
r_angle_refined_deg1.004
r_sphericity_free0.669
r_nbtor_refined0.305
r_symmetry_vdw_refined0.197
r_nbd_refined0.189
r_xyhbond_nbd_refined0.122
r_symmetry_hbond_refined0.093
r_chiral_restr0.073
r_bond_refined_d0.006
r_gen_planes_refined0.003
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_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13105
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms213

Software

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