4F6U

Crystal structure of human CDK8/CYCC in complex with compound 5 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(morpholin-4-yl)propyl]urea)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RGF	PDB ENTRY 3RGF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	293.15	20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.397	α = 90
b = 71.024	β = 90
c = 171.217	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		2011-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99987	SLS	X06SA

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	2.1	85.61	99.9	0.065		8.1	51652	51652

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	2.1	2.27	100		0.549		8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3RGF	2.1	85.61	51626	49911	1715	99.95	0.1772	0.1772	0.17649	0.19756	RANDOM	45.108

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]
-0.86			0.36		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.185
r_dihedral_angle_4_deg	13.861
r_dihedral_angle_3_deg	11.838
r_dihedral_angle_1_deg	5.509
r_scangle_it	5.509
r_scbond_it	3.774
r_mcangle_it	2.687
r_mcbond_it	1.569
r_angle_refined_deg	1.21
r_angle_other_deg	1.019

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.185
r_dihedral_angle_4_deg	13.861
r_dihedral_angle_3_deg	11.838
r_dihedral_angle_1_deg	5.509
r_scangle_it	5.509
r_scbond_it	3.774
r_mcangle_it	2.687
r_mcbond_it	1.569
r_angle_refined_deg	1.21
r_angle_other_deg	1.019
r_mcbond_other	0.453
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4986
Nucleic Acid Atoms
Solvent Atoms	309
Heterogen Atoms	92

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.