5J1W | pdb_00005j1w

Crystal structure of human CLK1 in complex with pyrido[3,4-g]quinazoline derivative ZW31 (compound 14)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	30% 1,2-propanediol, 10% glycerol and 50 mM Na/K phosphate pH 7.2

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.63	α = 90
b = 118.04	β = 99.55
c = 90.5	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	DECTRIS PILATUS3 6M		2014-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2.42	35.59	99.9	0.082	8.3	3.4		44729			53.1

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	2.42	2.55	99.9		0.599	2	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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		THROUGHOUT	2.42	35.59	42523	2159	99.78	0.19099	0.18916	0.2	0.22784	0.23	RANDOM	66.211

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]
-3.31		-1	3.32		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.883
r_dihedral_angle_4_deg	21.269
r_dihedral_angle_3_deg	14.911
r_long_range_B_other	7.889
r_long_range_B_refined	7.888
r_dihedral_angle_1_deg	6.468
r_scangle_other	5.781
r_mcangle_it	4.187
r_mcangle_other	4.186
r_scbond_it	3.706
r_scbond_other	3.705
r_mcbond_it	2.691
r_mcbond_other	2.691
r_angle_refined_deg	1.286
r_angle_other_deg	0.913
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8003
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	124

Software

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