3DOG | pdb_00003dog

Structure of Thr 160 phosphorylated CDK2/cyclin A in complex with the inhibitor N-&-N1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		unpublished phospho-CDK2/cyclin A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	ammonium sulphate, potassium chloride, HEPES pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.42	α = 90
b = 133.489	β = 90
c = 147.996	γ = 90

Symmetry
Space Group	P 21 21 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		2006-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.7	20	98.9	0.116	15.6			40784	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.85	96.3		0.412	3

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	CDK2/cyclin A	2.7	20	40784	38582	2037	98.7	0.197	0.19927	0.19673	0.212	0.24758	0.2584	RANDOM	7.307

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]
-0.95			-0.47		1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.258
r_dihedral_angle_3_deg	16.894
r_dihedral_angle_4_deg	15.905
r_dihedral_angle_1_deg	5.712
r_scangle_it	1.41
r_angle_refined_deg	1.267
r_scbond_it	0.827
r_mcangle_it	0.71
r_mcbond_it	0.449
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.294
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.166
r_symmetry_vdw_refined	0.161
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8803
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing