3W80

Crystal structure of dodecamer human insulin with double C-axis length of the hexamer 2 Zn insulin cell


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3W7Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.6729310mg/ml protein, 0.1M Sodium Citrate, 22%(v/v) DMF, 0.08%(w/v) Zinc chloride, pH 8.67, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9336.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.72α = 90
b = 82.72β = 90
c = 68.14γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEFully automatic high speed Weissenberg data collection system called GalaxyThe vertically focusing 1m long bent mirror of Pt-coated fused silica is 21m from the SR source point and 7m from the focus point2003-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6C1.00Photon FactoryBL-6C

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
11500.054764.4690240

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 REPLACEMENTTHROUGHOUT3w7y1.41032370170099.460.185390.18220.24845RANDOM24.619
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]
0.050.050.05-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free49.868
r_dihedral_angle_2_deg35.54
r_sphericity_bonded22.922
r_dihedral_angle_3_deg11.746
r_dihedral_angle_4_deg6.368
r_dihedral_angle_1_deg5.562
r_rigid_bond_restr2.889
r_angle_refined_deg1.258
r_chiral_restr0.082
r_bond_refined_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free49.868
r_dihedral_angle_2_deg35.54
r_sphericity_bonded22.922
r_dihedral_angle_3_deg11.746
r_dihedral_angle_4_deg6.368
r_dihedral_angle_1_deg5.562
r_rigid_bond_restr2.889
r_angle_refined_deg1.258
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1620
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms4

Software

Software
Software NamePurpose
WEISdata scaling
CCP4model building
REFMACrefinement
WEISdata reduction
CCP4phasing