5FGK | pdb_00005fgk

CDK8-CYCC IN COMPLEX WITH 8-[3-(3-Amino-1H-indazol-6-yl)-5-chloro- pyridine-4-yl]-2,8-diaza-spiro[4.5]decan-1-one

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	RESERVOIR SOLUTION : pH 6.90

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.943	α = 90
b = 71.928	β = 90
c = 177.926	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	110	PIXEL	DECTRIS PILATUS 6M		2012-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00008	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.36	88.96	97.4	0.082	0.1	9.17	2.8		38677			48.365

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.61	99.1		0.483	0.043	2.31	2.8

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	NONE	2.36	88.96	36455	1208	97.38		0.22	0.2369	0.24	RANDOM	34.592

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]
2			-1.9		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.312
r_dihedral_angle_4_deg	14.52
r_dihedral_angle_3_deg	12.825
r_scangle_it	5.753
r_dihedral_angle_1_deg	5.661
r_scbond_it	4.102
r_mcangle_it	2.678
r_mcbond_it	1.587
r_angle_refined_deg	1.252
r_angle_other_deg	1.038

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.312
r_dihedral_angle_4_deg	14.52
r_dihedral_angle_3_deg	12.825
r_scangle_it	5.753
r_dihedral_angle_1_deg	5.661
r_scbond_it	4.102
r_mcangle_it	2.678
r_mcbond_it	1.587
r_angle_refined_deg	1.252
r_angle_other_deg	1.038
r_mcbond_other	0.403
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4952
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	61

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.