4F7N | pdb_00004f7n

Crystal structure of human CDK8/CYCC in complex with compound 11 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(5-hydroxypentyl)urea)

X-RAY DIFFRACTION

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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
2.89	57.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.157	α = 90
b = 71.76	β = 90
c = 180.362	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		2012-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00001	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	2.65	90.19	99.7	0.076	8.5	3.7	27863	27863

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	2.65	2.86	99.6		0.515	1.4	3.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3RGF	2.65	90.19	27863	26899	908	99.63	0.19986	0.19986	0.19893	0.21	0.22794	0.24	RANDOM	59.491

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]
1.43			-1.78		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.138
r_dihedral_angle_4_deg	15.202
r_dihedral_angle_3_deg	12.227
r_dihedral_angle_1_deg	5.29
r_scangle_it	3.803
r_scbond_it	2.607
r_mcangle_it	1.741
r_mcbond_it	1.418
r_angle_refined_deg	1.178
r_angle_other_deg	0.931
r_mcbond_other	0.212
r_nbd_refined	0.171
r_nbtor_refined	0.162
r_symmetry_vdw_other	0.133
r_nbd_other	0.132
r_symmetry_hbond_refined	0.129
r_xyhbond_nbd_refined	0.108
r_symmetry_vdw_refined	0.083
r_nbtor_other	0.075
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4993
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	34

Software

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