6Z53 | pdb_00006z53

Crystal structure of CLK3 in complex with macrocycle ODS2003128

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EU9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	20% PEG 3350, 0.2 M Na/K phosphate, 10% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.995	α = 90
b = 62.5	β = 97.67
c = 76.027	γ = 90

Symmetry
Space Group	C 1 2 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	DECTRIS PILATUS3 2M		2012-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9200	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.65	37.87	96.4	0.053	0.065	0.036	10.5	2.9		48435

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.74	97.4		0.585	0.585	0.715	0.404	2.5	2.9

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 (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2eu9	1.65	37.87	45983	2443	95.89	0.1685	0.167	0.1945	0.2398	RANDOM	16.945

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]
0.58		0.49	-0.46		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.918
r_dihedral_angle_4_deg	18.724
r_dihedral_angle_3_deg	13.342
r_dihedral_angle_1_deg	5.516
r_angle_refined_deg	1.733
r_angle_other_deg	0.992
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2896
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms	98

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing