6GU6

CDK1/Cks2 in complex with Dinaciclib

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YC6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	CONDITIONS AROUND 0.1M BIS-TRIS(PH6.5), 0.2M SODIUM NITRATE 20% PEG3350, PROTEIN AT 10-12 MG/ML, 0.5Mm INHIBITOR

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.704	α = 90
b = 97.232	β = 90
c = 108.564	γ = 90

Symmetry
Space Group	I 2 2 2

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		2016-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.987	Diamond	I24

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	2.33	72.43	99.8	0.05	10.8	1.9		21580

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	2.33	2.41	97.7		0.42	2.4	1.9

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	4YC6	2.33	72.43	20503	1077	99.78	0.20317	0.20092	0.24586	RANDOM	47.498

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]
1.9			-1.73		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.208
r_dihedral_angle_4_deg	20.6
r_dihedral_angle_3_deg	18.415
r_long_range_B_other	9.98
r_long_range_B_refined	9.975
r_dihedral_angle_1_deg	7.635
r_scangle_other	7.605
r_mcangle_it	6.103
r_mcangle_other	6.101
r_scbond_it	4.905
r_scbond_other	4.905
r_mcbond_other	4.049
r_mcbond_it	4.048
r_angle_other_deg	3.598
r_angle_refined_deg	1.85
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_other	0.009
r_gen_planes_refined	0.008
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2943
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	29

Software

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