9ET4 | pdb_00009et4

CDK2-cyclin A in complex with FragLite 9

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
2.77	55.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.832	α = 90
b = 133.2	β = 90
c = 147.089	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	2.62	133.2	96.9	0.3	0.323	0.12	0.994	6.2	13.6		43095

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	2.62	2.72			2.803	3.011	1.098	0.718	0.7	14.4

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	2.641	98.928	41560	2076	95.813	0.22	0.2202	0.2202	0.2216	0.2213	63.877

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]
-3.272			2.11		1.162

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.098
r_dihedral_angle_6_deg	16.544
r_dihedral_angle_3_deg	15.317
r_lrange_it	12.149
r_scangle_it	8.791
r_mcangle_it	6.531
r_dihedral_angle_1_deg	6.118
r_scbond_it	5.845
r_mcbond_it	4.141
r_angle_refined_deg	1.625

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.098
r_dihedral_angle_6_deg	16.544
r_dihedral_angle_3_deg	15.317
r_lrange_it	12.149
r_scangle_it	8.791
r_mcangle_it	6.531
r_dihedral_angle_1_deg	6.118
r_scbond_it	5.845
r_mcbond_it	4.141
r_angle_refined_deg	1.625
r_nbtor_refined	0.318
r_symmetry_xyhbond_nbd_refined	0.316
r_symmetry_nbd_refined	0.314
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.095
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8923
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	66

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.