2BRF

Crystal Structure of the FHA Domain of Human Polynucleotide Kinase 3' Phosphatase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UJXPDB ENTRY 1UJX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1PROTEIN WAS CRYSTALLISED IN 0.1 M TRIS-HCL PH 8.5, 2.0 M AMMONIUM SULPHATE
Crystal Properties
Matthews coefficientSolvent content
237.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.812α = 90
b = 40.047β = 90.96
c = 37.512γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.437.597.20.058.93.416490
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)
11.41.44880.163.92.4

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 1UJX1.437.515643834880.1520.150.183RANDOM8.84
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]
-0.330.020.060.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.932
r_dihedral_angle_4_deg11.591
r_dihedral_angle_3_deg10.403
r_dihedral_angle_1_deg6.85
r_scangle_it4.68
r_scbond_it3.671
r_angle_refined_deg2.512
r_mcangle_it2.23
r_mcbond_it2.104
r_angle_other_deg1.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.932
r_dihedral_angle_4_deg11.591
r_dihedral_angle_3_deg10.403
r_dihedral_angle_1_deg6.85
r_scangle_it4.68
r_scbond_it3.671
r_angle_refined_deg2.512
r_mcangle_it2.23
r_mcbond_it2.104
r_angle_other_deg1.068
r_xyhbond_nbd_refined0.445
r_symmetry_vdw_other0.324
r_symmetry_vdw_refined0.289
r_symmetry_hbond_refined0.289
r_nbd_refined0.245
r_nbd_other0.207
r_chiral_restr0.187
r_nbtor_refined0.166
r_nbtor_other0.089
r_bond_refined_d0.03
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms755
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing