3FZ1

Crystal structure of a benzthiophene inhibitor bound to human Cyclin-dependent Kinase-2 (CDK-2)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	CDK-1 at 2.5 mg/ml is equilibrated against a well solution containing 14% PEG 4000, 50 mM ammonium acetate, 50 mM Hepes pH 7.5, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.717	α = 90
b = 71.709	β = 90
c = 72.242	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++		2005-01-07		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	30	99	0.04	29.843	4.2		22384

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	98.9		0.334		3.7	2185

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1AQ1	1.9	27.66	22346	1147	98.96	0.212	0.21	0.259	RANDOM	30.062

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]
-0.07			0.24		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.287
r_dihedral_angle_4_deg	17.684
r_dihedral_angle_3_deg	14.544
r_dihedral_angle_1_deg	4.998
r_scangle_it	3.15
r_scbond_it	1.923
r_mcangle_it	1.473
r_angle_refined_deg	1.21
r_mcbond_it	0.8
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.287
r_dihedral_angle_4_deg	17.684
r_dihedral_angle_3_deg	14.544
r_dihedral_angle_1_deg	4.998
r_scangle_it	3.15
r_scbond_it	1.923
r_mcangle_it	1.473
r_angle_refined_deg	1.21
r_mcbond_it	0.8
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2284
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	19

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.