3EJ1 | pdb_00003ej1

CDK2/CyclinA complexed with a pyrazolopyridazine inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FVV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	277	1.5 M sodium acetate, 100 mM sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.09	69.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.776	α = 90
b = 183.776	β = 90
c = 214.045	γ = 120

Symmetry
Space Group	P 62 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	MAR CCD 165 mm		2000-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	3.22	160.13	98	0.14	22	13.9	32959	32959	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)
1	3.22	3.3	95		0.67	2.1	12.2	2297

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	1FVV	3.22	160.13	32959	32959	1737	98.64	0.22099	0.22099	0.219	0.2161	0.25887	0.2567	RANDOM	69.353

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]
3.85	1.93		3.85		-5.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.379
r_dihedral_angle_3_deg	16.099
r_dihedral_angle_4_deg	15.586
r_dihedral_angle_1_deg	5.149
r_angle_refined_deg	1.112
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.205
r_nbd_refined	0.195
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_mcbond_it
r_mcangle_it
r_scbond_it
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8788
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	38

Software

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