X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O08PDB entry 3O08

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82921microL reservoir + 1microL protein; reservoir: 22% PEG6000, 0.1M Tris pH 8.0, protein: 10mg/ml KlHxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF , VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.6253.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.503α = 90
b = 57.036β = 110.34
c = 72.811γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMAR scanner 345 mm plate2004-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.83082.70.0679.42.111502-349.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.962.40.1712.21.5858

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 3O082.829.7610484101882.750.182880.177650.23755RANDOM60.091
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]
-5.68-2.827.63-3.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.017
r_dihedral_angle_4_deg16.655
r_dihedral_angle_3_deg16.54
r_dihedral_angle_1_deg4.499
r_scangle_it1.964
r_scbond_it1.142
r_angle_refined_deg0.956
r_mcangle_it0.731
r_mcbond_it0.376
r_chiral_restr0.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.017
r_dihedral_angle_4_deg16.655
r_dihedral_angle_3_deg16.54
r_dihedral_angle_1_deg4.499
r_scangle_it1.964
r_scbond_it1.142
r_angle_refined_deg0.956
r_mcangle_it0.731
r_mcbond_it0.376
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.003
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 Atoms3708
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling