7ZPC | pdb_00007zpc

CDK2 in complex 9K-DOS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MHQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	10MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.211	α = 90
b = 71.98	β = 90
c = 72.068	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		2021-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.898	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.4	50.981	100	0.022	1	28.2	11.8		55242

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	100		0.47	1		12.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5MHQ	1.4	50.981	55172	2735	99.964	0.202	0.2014	0.2014	0.2211	0.2212	26.987

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]
-0.568			1.199		-0.631

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.322
r_dihedral_angle_6_deg	17.21
r_dihedral_angle_3_deg	16.934
r_lrange_it	8.26
r_dihedral_angle_1_deg	6.291
r_scangle_it	5.121
r_mcangle_it	3.554
r_scbond_it	3.313
r_mcbond_it	2.557
r_angle_refined_deg	1.815
r_nbtor_refined	0.329
r_symmetry_nbd_refined	0.296
r_nbd_refined	0.247
r_symmetry_xyhbond_nbd_refined	0.201
r_xyhbond_nbd_refined	0.191
r_chiral_restr	0.096
r_gen_planes_refined	0.013
r_bond_refined_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2347
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	24

Software

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