3I6W | pdb_00003i6w

Structure and Activation Mechanism of the CHK2 DNA-Damage Checkpoint Kinase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I6U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	1:1 ratio mix of protein solution (~12 mg/ml protein in 20 mM Tris-HCl, 150 mM NaCl, 10 mM dithiothreitol (DTT), 3% (v/v) glycerol, pH 8.0 and well bufffer (100 mM NaHepes, 300 mM Ammonium Tartrate, 22% PEG 3350, pH 7.0). Crystals were flash frozen in crystallization buffer supplemented with 16-20% (v/v) glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.2	α = 84.1
b = 114.7	β = 81.2
c = 123	γ = 80.7

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 315		2006-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E		APS	24-ID-E

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	3.25	30	96.2	0.042		1.8		60983

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3I6U	3.25	30	56117	1755	90.8	0.252	0.251	0.24	0.287	RANDOM	137.5

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]
-0.26	-0.34	1.73	-3.09	-3.45	3.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.202
r_dihedral_angle_4_deg	21.623
r_dihedral_angle_3_deg	19.937
r_dihedral_angle_1_deg	5.446
r_scangle_it	4.357
r_scbond_it	2.596
r_mcangle_it	2.574
r_mcbond_it	1.442
r_angle_refined_deg	1.138
r_symmetry_hbond_refined	0.626
r_symmetry_vdw_refined	0.619
r_nbtor_refined	0.31
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
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 Atoms	Number
Protein Atoms	24560
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement