1Z57 | pdb_00001z57

Crystal structure of human CLK1 in complex with 10Z-Hymenialdisine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JOW	1JOW.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	277	PEG 6K, Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.277	α = 90
b = 64.434	β = 119.19
c = 80.112	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	CCD	MARMOSAIC 225 mm CCD		2005-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9184	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	50	99.8				45196

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.75	86

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 (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	1JOW.pdb	1.7	29.3	40775	40775	2173	95.01	0.14014	0.13765	0.15	0.18581	0.2	RANDOM	18.72

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]
0.48		0.46	-0.58		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.84
r_dihedral_angle_4_deg	20.028
r_dihedral_angle_3_deg	11.532
r_sphericity_free	7.032
r_scangle_it	6.814
r_dihedral_angle_1_deg	5.85
r_scbond_it	5.216
r_mcangle_it	4.35
r_sphericity_bonded	3.696
r_mcbond_it	3.679
r_rigid_bond_restr	2.634
r_mcbond_other	2.161
r_angle_refined_deg	1.591
r_angle_other_deg	0.845
r_symmetry_vdw_other	0.325
r_nbd_refined	0.221
r_nbd_other	0.179
r_nbtor_refined	0.176
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.095
r_symmetry_hbond_refined	0.095
r_nbtor_other	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2674
Nucleic Acid Atoms
Solvent Atoms	401
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing