7OA0 | pdb_00007oa0

Crystal structure of di-phosphorylated human CLK1 in complex with 5-(6,7-dichloro-1H-indol-3-yl)pyrimidin-4-amine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6R8J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	24% PEG3350, 200mM MgCl2, 100mM BisTris (pH 6.5)

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.22	α = 90
b = 68.22	β = 90
c = 283.14	γ = 120

Symmetry
Space Group	P 65 2 2

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 6M		2016-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.976	ESRF	ID23-1

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	1.81	100	99.7	0.066	20.68	5.73		36760

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.81	1.87	99.8		1.17	0.679

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6R8J	1.81	50.128	36755	1837	99.704	0.195	0.1926	0.2	0.2423	0.25	38.601

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]
0.911	0.455		0.911		-2.955

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.034
r_dihedral_angle_4_deg	19.422
r_dihedral_angle_3_deg	15.132
r_lrange_it	8.635
r_lrange_other	8.619
r_scangle_it	7.348
r_scangle_other	7.346
r_dihedral_angle_1_deg	7.152
r_scbond_it	5.168
r_scbond_other	5.166
r_mcangle_other	4.857
r_mcangle_it	4.856
r_mcbond_it	3.882
r_mcbond_other	3.878
r_angle_refined_deg	1.849
r_angle_other_deg	1.44
r_nbd_other	0.229
r_nbd_refined	0.223
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.174
r_xyhbond_nbd_refined	0.166
r_symmetry_nbd_refined	0.098
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2719
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	18

Software

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