2OMI

Structure of human insulin cocrystallized with protamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OMGinsulin hexamer R-conformation

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.329150mM resorcinol, 400mM NaCl, 1.0mg/ml protamine 30mM phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.346.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.52α = 90
b = 61.84β = 90
c = 86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2005-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.918SLSX06SA

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
12.243098.60.10712.16.5161061588133.7
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)
2.242.497.60.2864.12.82781

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 REPLACEMENTTHROUGHOUTinsulin hexamer R-conformation2.2429.11508779398.640.202760.199290.26838RANDOM26.301
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]
0.06-0.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.831
r_dihedral_angle_3_deg17
r_dihedral_angle_4_deg14.14
r_dihedral_angle_1_deg7.492
r_scangle_it5.135
r_scbond_it3.407
r_mcangle_it2.348
r_angle_refined_deg1.941
r_mcbond_it1.548
r_xyhbond_nbd_refined0.345
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.831
r_dihedral_angle_3_deg17
r_dihedral_angle_4_deg14.14
r_dihedral_angle_1_deg7.492
r_scangle_it5.135
r_scbond_it3.407
r_mcangle_it2.348
r_angle_refined_deg1.941
r_mcbond_it1.548
r_xyhbond_nbd_refined0.345
r_nbtor_refined0.312
r_symmetry_hbond_refined0.231
r_nbd_refined0.225
r_symmetry_vdw_refined0.221
r_metal_ion_refined0.205
r_chiral_restr0.154
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2349
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing