1YJM | pdb_00001yjm

Crystal structure of the FHA domain of mouse polynucleotide kinase in complex with an XRCC4-derived phosphopeptide.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YJ5	The FHA domain from the full-length mouse PNK structure, 1YJ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.1M Na citrate (pH 5.5), 25% PEG 4000, 0.2M Li2SO4, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.155	α = 90
b = 122.999	β = 90
c = 136.71	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2004-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1159	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	50	89.4	0.051	8.8	2.7	21246	18994	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	70.2		0.194	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	The FHA domain from the full-length mouse PNK structure, 1YJ5	2.2	50	21246	18994	1022	89.49	0.21253	0.21253	0.21088	0.22	0.24278	0.24	RANDOM	25.637

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]
0.21			-0.74		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.548
r_dihedral_angle_3_deg	10.997
r_dihedral_angle_4_deg	10.402
r_dihedral_angle_1_deg	5.026
r_angle_refined_deg	0.862
r_angle_other_deg	0.669
r_scangle_it	0.43
r_scbond_it	0.282
r_mcangle_it	0.208
r_mcbond_it	0.192
r_symmetry_vdw_refined	0.167
r_nbd_refined	0.163
r_nbtor_refined	0.157
r_nbd_other	0.149
r_symmetry_vdw_other	0.101
r_xyhbond_nbd_refined	0.082
r_symmetry_hbond_refined	0.077
r_nbtor_other	0.07
r_chiral_restr	0.055
r_mcbond_other	0.022
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2531
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing