1Y8Y | pdb_00001y8y

Crystal structure of human CDK2 complexed with a pyrazolo[1,5-a]pyrimidine inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B39	pdb entry 1B39

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	PEG 3350, Hepes, Ammonium acetate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.9	34.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.944	α = 90
b = 71.756	β = 90
c = 71.957	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	IMAGE PLATE	RIGAKU RAXIS IV++	mirrors	2003-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	1.9	50	95.8	0.054	11	2.5	22465	22465	1	1	28

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)
	1.9	1.97	82.4		0.262	1.3	1.73	2215

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	pdb entry 1B39	1.996	50.64	1	19296	17489	1616	99.31	0.19404	0.19404	0.1871	0.1938	0.27216	0.2739	RANDOM	38.439

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]
0.27			1.09		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.569
r_scangle_it	4.464
r_scbond_it	2.981
r_mcangle_it	1.914
r_angle_refined_deg	1.892
r_mcbond_it	1.133
r_symmetry_vdw_refined	0.275
r_nbd_refined	0.239
r_symmetry_hbond_refined	0.214
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.129
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2345
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling
MOLREP	phasing