9PE7 | pdb_00009pe7

CDK6 to CDK4 active site surrogate in complex with compound 6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in-house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		286.15	Well volume: 100.0 uL Well Ingredients: Precipitant: 4.0 %w/v (8.0 uL of stock 50.0 %w/v) PEG 3350 Salt: 5.0 mM (5.0 uL of stock 100.0 mM) Calcium chloride dihydrate Salt: 0.0928571429 M (9.2857142857 uL of stock 1.0 M) Ammonium Nitrate Plate setup temperature: 21 C Plate incubation temperature: 13 C Drop volume from well: 1.0 uL Drop protein volume: 1.0 uL Protein formulation name: LJIC-3730A1 + PF-6825089 b Protein Formulation Composition: Protein: CDK6 mutated to look like CDK4 (6.87 mg/mL) Compound: PF-6825089 (1.00 mM)

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.44	α = 90
b = 101.44	β = 90
c = 59.8	γ = 90

Symmetry
Space Group	I 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS PILATUS 6M		2018-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.05	29.9	97.86	0.999	22.77	6.7		19156

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.12	81.59		0.843

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.05	29.9	18770	901	97.9	0.2156	0.213	0.2031	0.2672	0.2598	RANDOM	42.39

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]
0.3473			0.3473		-0.6945

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.46
t_omega_torsion	3.22
t_angle_deg	0.94
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2098
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	33

Software

Software
Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
BUSTER	phasing