2J90

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YRPPDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX
experimental modelPDB 1JKTPDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX
experimental modelPDB 1JKSPDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX
experimental modelPDB 1WVXPDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1830% PEG 1000 0.1M SPG BUFFER PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.4750.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.765α = 90
b = 95.765β = 90
c = 150.941γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
125099.80.088.75.648089-335
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.071000.6725.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX25045599243399.80.1870.1850.222RANDOM30.5
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]
-0.73-0.731.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.912
r_dihedral_angle_4_deg16.202
r_dihedral_angle_3_deg13.705
r_scangle_it5.859
r_dihedral_angle_1_deg5.169
r_scbond_it3.998
r_mcangle_it2.556
r_mcbond_it1.742
r_angle_other_deg1.239
r_angle_refined_deg1.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.912
r_dihedral_angle_4_deg16.202
r_dihedral_angle_3_deg13.705
r_scangle_it5.859
r_dihedral_angle_1_deg5.169
r_scbond_it3.998
r_mcangle_it2.556
r_mcbond_it1.742
r_angle_other_deg1.239
r_angle_refined_deg1.147
r_symmetry_vdw_other0.294
r_nbd_refined0.197
r_nbd_other0.18
r_nbtor_refined0.173
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.129
r_symmetry_hbond_refined0.123
r_nbtor_other0.082
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms4189
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing