2J90

Crystal structure of human ZIP kinase in complex with a tetracyclic pyridone inhibitor (Pyridone 6)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YRP	PDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX
experimental model	PDB	1JKT	PDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX
experimental model	PDB	1JKS	PDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX
experimental model	PDB	1WVX	PDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		30% PEG 1000 0.1M SPG BUFFER PH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.765	α = 90
b = 95.765	β = 90
c = 150.941	γ = 90

Symmetry
Space Group	P 43 21 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	CCD	MARRESEARCH		2006-09-23	M	SINGLE WAVELENGTH

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

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	50	99.8	0.08	8.7	5.6		48089		-3	35

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	2.07	100		0.67	2	5.6

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX	2	50	45599	2433	99.8	0.187	0.185	0.19	0.222	0.22	RANDOM	30.5

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]
-0.73			-0.73		1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.912
r_dihedral_angle_4_deg	16.202
r_dihedral_angle_3_deg	13.705
r_scangle_it	5.859
r_dihedral_angle_1_deg	5.169
r_scbond_it	3.998
r_mcangle_it	2.556
r_mcbond_it	1.742
r_angle_other_deg	1.239
r_angle_refined_deg	1.147
r_symmetry_vdw_other	0.294
r_nbd_refined	0.197
r_nbd_other	0.18
r_nbtor_refined	0.173
r_symmetry_vdw_refined	0.159
r_xyhbond_nbd_refined	0.129
r_symmetry_hbond_refined	0.123
r_nbtor_other	0.082
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
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
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4189
Nucleic Acid Atoms
Solvent Atoms	327
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing