9ESX | pdb_00009esx

CDK2-cyclin A in complex with FragLite 17

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GUC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	Protein at 10 mg/ml. 0.6 to 0.8 M KCl, 0.9 to 1.2 M (NH4)2SO4, and 100 mM HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.124	α = 90
b = 133.905	β = 90
c = 147.584	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	PIXEL	DECTRIS PILATUS 6M		2020-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.89842	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.37	147.58	93.5	0.172	0.185	0.05	0.998	10.6	13.5		56614

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.37	2.44	100		2.064	2.234	0.624	0.568	1.2	13.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.37	73.901	55818	2848	92.365	0.222	0.222	0.2176	0.2292	0.2214	34.791

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]
-2.28			-0.291		2.571

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.42
r_dihedral_angle_3_deg	15.609
r_dihedral_angle_2_deg	13.667
r_lrange_it	10.091
r_scangle_it	7.715
r_mcangle_it	5.634
r_dihedral_angle_1_deg	5.477
r_scbond_it	5.24
r_mcbond_it	3.628
r_angle_refined_deg	1.582

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.42
r_dihedral_angle_3_deg	15.609
r_dihedral_angle_2_deg	13.667
r_lrange_it	10.091
r_scangle_it	7.715
r_mcangle_it	5.634
r_dihedral_angle_1_deg	5.477
r_scbond_it	5.24
r_mcbond_it	3.628
r_angle_refined_deg	1.582
r_nbtor_refined	0.316
r_nbd_refined	0.219
r_symmetry_nbd_refined	0.21
r_symmetry_xyhbond_nbd_refined	0.187
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.093
r_bond_refined_d	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8967
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.