4C59

Structure of GAK kinase in complex with nanobody (NbGAK_4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LL6PDB ENTRIES 3LL6 AND 1OP9
experimental modelPDB 1OP9PDB ENTRIES 3LL6 AND 1OP9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.59% PEG 3350, 0.06 M MAGNESIUM FORMATE, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 174.268α = 90
b = 37.753β = 111.46
c = 75.546γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2012-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.819.7599.50.148.33.6115802
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)
12.82.9599.80.6923.7

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 3LL6 AND 1OP92.819.751102854999.290.205160.202380.26163RANDOM60.577
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]
-2.262.81-0.391.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.511
r_dihedral_angle_4_deg19.83
r_dihedral_angle_3_deg15.166
r_dihedral_angle_1_deg6.191
r_mcangle_it2.145
r_scbond_it1.429
r_mcbond_it1.256
r_mcbond_other1.256
r_angle_refined_deg1.048
r_angle_other_deg0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.511
r_dihedral_angle_4_deg19.83
r_dihedral_angle_3_deg15.166
r_dihedral_angle_1_deg6.191
r_mcangle_it2.145
r_scbond_it1.429
r_mcbond_it1.256
r_mcbond_other1.256
r_angle_refined_deg1.048
r_angle_other_deg0.65
r_chiral_restr0.061
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms2957
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing