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
5.08959775.833054

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 252.26α = 90
b = 252.26β = 90
c = 111.376γ = 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
135097.90.11711.15.779287
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)
33.1195.10.5075.47673

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 3KT0349.0475143398897.790.248080.246780.27307RANDOM80.62
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]
-3.3-1.65-3.34.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.223
r_dihedral_angle_3_deg14.229
r_dihedral_angle_4_deg12.351
r_dihedral_angle_1_deg4.73
r_mcangle_it1.436
r_mcbond_it1.232
r_angle_refined_deg0.857
r_nbtor_refined0.296
r_scangle_it0.261
r_scbond_it0.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.223
r_dihedral_angle_3_deg14.229
r_dihedral_angle_4_deg12.351
r_dihedral_angle_1_deg4.73
r_mcangle_it1.436
r_mcbond_it1.232
r_angle_refined_deg0.857
r_nbtor_refined0.296
r_scangle_it0.261
r_scbond_it0.165
r_symmetry_vdw_refined0.16
r_nbd_refined0.155
r_xyhbond_nbd_refined0.104
r_chiral_restr0.059
r_symmetry_hbond_refined0.059
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_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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13091
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms110

Software

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