X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.52921MICROL RESERVOIR + 1MICROL PROTEIN, RESERVOIR: 2.5M AMMONIA SULFATE, 0.1M CHES PH 9.5, 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
2.7354.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.71α = 90
b = 91.99β = 110.92
c = 92.58γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateSi, coated with 200 layers of Mo/Si2005-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9537BESSY14.2

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
11.6130870.06218.55.3149205129734-324.3
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)
1.611.6598.70.5083.23.310853

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 3O081.6129.2128436129387.050.169920.169430.21996RANDOM19.265
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]
0.530.430.05-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.057
r_dihedral_angle_4_deg19.111
r_dihedral_angle_3_deg13.964
r_scangle_it6.848
r_dihedral_angle_1_deg5.978
r_scbond_it4.559
r_mcangle_it2.858
r_angle_refined_deg2.094
r_mcbond_it1.985
r_chiral_restr0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.057
r_dihedral_angle_4_deg19.111
r_dihedral_angle_3_deg13.964
r_scangle_it6.848
r_dihedral_angle_1_deg5.978
r_scbond_it4.559
r_mcangle_it2.858
r_angle_refined_deg2.094
r_mcbond_it1.985
r_chiral_restr0.14
r_bond_refined_d0.023
r_gen_planes_refined0.013
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 Atoms7526
Nucleic Acid Atoms
Solvent Atoms819
Heterogen Atoms154

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling