6V6L

Co-structure of human glycogen synthase kinase beta with 1-(6-((2-((6-amino-5-nitropyridin-2-yl)amino)ethyl)amino)-2-(2,4-dichlorophenyl)pyridin-3-yl)-4-methylpiperazin-2-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6B8J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2907-12% (w:v) PEG 6000 and 5-8% MPD (v:v)
Crystal Properties
Matthews coefficientSolvent content
2.1242.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.08α = 90
b = 64.76β = 100.13
c = 58.25γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray290IMAGE PLATERIGAKU RAXIS IV2006-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
12.1925.0196.90.1097.32.520146
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)
12.192.250.614

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 REPLACEMENTTHROUGHOUT6B8J2.1924.1720146101596.40.2040.2030.234RANDOM29.4
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]
-0.0352-4.6723-3.35063.3858
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.03
t_omega_torsion2.58
t_angle_deg1.04
t_bond_d0.008
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.03
t_omega_torsion2.58
t_angle_deg1.04
t_bond_d0.008
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2683
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms41

Software

Software
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
CrystalCleardata collection
CNSphasing