2OMG

Structure of human insulin cocrystallized with protamine and urea


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7INSinsulin trimer R-conformation

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.329160mM m-cresol, 3M urea, 1.0 mg/ml protamine sulphate, 400mM NaCl, 40mM phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3347.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.66α = 90
b = 61.66β = 90
c = 85.54γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2004-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-50.969MAX III911-5

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
11.5250930.08214.48270222511930.5
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)
11.521.674.70.334.964630

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 trimer R-conformation1.5225.8823837127695.990.183910.182530.20947RANDOM28.01
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.987
r_dihedral_angle_3_deg11.45
r_dihedral_angle_4_deg8.404
r_dihedral_angle_1_deg6.769
r_scangle_it4.054
r_scbond_it2.61
r_mcangle_it1.667
r_angle_refined_deg1.545
r_angle_other_deg0.945
r_mcbond_it0.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.987
r_dihedral_angle_3_deg11.45
r_dihedral_angle_4_deg8.404
r_dihedral_angle_1_deg6.769
r_scangle_it4.054
r_scbond_it2.61
r_mcangle_it1.667
r_angle_refined_deg1.545
r_angle_other_deg0.945
r_mcbond_it0.935
r_symmetry_vdw_refined0.334
r_symmetry_hbond_refined0.305
r_xyhbond_nbd_refined0.294
r_nbd_refined0.289
r_mcbond_other0.287
r_nbtor_refined0.205
r_nbd_other0.195
r_symmetry_vdw_other0.187
r_metal_ion_refined0.184
r_chiral_restr0.103
r_nbtor_other0.09
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1163
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing