9ESK | pdb_00009esk

CDK2-cyclin A in complex with FragLite 30

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
2.82	56.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.092	α = 90
b = 134.078	β = 90
c = 147.75	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	2.38	147.75	91.3	0.171	0.185	0.069	0.998	10	13.5		54691

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	2.38	2.45	100		2.466	2.667	1.011	0.466	1	13.4

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	2.398	73.984	52891	2680	90.41	0.211	0.211	0.1981	0.217	0.1991	63.034

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]
0.814			-0.287		-0.528

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.746
r_dihedral_angle_6_deg	16.98
r_dihedral_angle_3_deg	16.087
r_lrange_it	12.73
r_scangle_it	9.319
r_mcangle_it	7.198
r_scbond_it	6.407
r_dihedral_angle_1_deg	5.913
r_mcbond_it	4.819
r_angle_refined_deg	1.594
r_symmetry_nbd_refined	0.323
r_nbtor_refined	0.314
r_symmetry_xyhbond_nbd_refined	0.239
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.1
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9026
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	96

Software

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