3RGF

Crystal Structure of human CDK8/CycC

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZP2	PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH
experimental model	PDB	2I53	PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH
experimental model	PDB	2PK2	PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH
experimental model	PDB	2WH2	PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH
experimental model	PDB	2RK3	PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH
experimental model	PDB	2UZE	PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH
experimental model	PDB	2R3Q	PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH
experimental model	PDB	2R3N	PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH
experimental model	PDB	2VTH	PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% PEG3350, 0.2M lithium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.69	α = 90
b = 70.61	β = 108.31
c = 79.14	γ = 90

Symmetry
Space Group	P 1 21 1

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	PSI PILATUS 6M		2010-05-10	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	37.567	100	0.089	0.089	10.7	4.6		37725

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	99.9		0.542	0.542	2.6	4.6

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	PDB ENTRIES 1ZP2, 2I53, 2PK2, 2WH2, 2PK2, 2RK3, 2UZE, 2R3Q, 2R3N, 2VTH	2.2	37.567	37691	1885	99.92	0.1826	0.1805	0.2209	RANDOM	44.536

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]
-0.51		0.17	0.86		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.679
r_dihedral_angle_4_deg	14.94
r_dihedral_angle_3_deg	12.431
r_scangle_it	5.325
r_dihedral_angle_1_deg	5.018
r_scbond_it	3.49
r_mcangle_it	2.394
r_mcbond_it	1.346
r_angle_refined_deg	1.004
r_angle_other_deg	0.802
r_mcbond_other	0.333
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4869
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	82

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
RemDAq	data collection
BALBES	phasing