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Structure of human insulin cocrystallized with protamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OMG insulin hexamer R-conformation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 291 50mM resorcinol, 400mM NaCl, 1.0mg/ml protamine 30mM phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.3 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.52 α = 90 b = 61.84 β = 90 c = 86 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2005-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.918 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.24 30 98.6 0.107 12.1 6.5 16106 15881 33.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.24 2.4 97.6 0.286 4.1 2.8 2781
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT insulin hexamer R-conformation 2.24 29.1 15087 793 98.64 0.20276 0.19929 0.1955 0.26838 0.2603 RANDOM 26.301
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.831 r_dihedral_angle_3_deg 17 r_dihedral_angle_4_deg 14.14 r_dihedral_angle_1_deg 7.492 r_scangle_it 5.135 r_scbond_it 3.407 r_mcangle_it 2.348 r_angle_refined_deg 1.941 r_mcbond_it 1.548 r_xyhbond_nbd_refined 0.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.831 r_dihedral_angle_3_deg 17 r_dihedral_angle_4_deg 14.14 r_dihedral_angle_1_deg 7.492 r_scangle_it 5.135 r_scbond_it 3.407 r_mcangle_it 2.348 r_angle_refined_deg 1.941 r_mcbond_it 1.548 r_xyhbond_nbd_refined 0.345 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.231 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.221 r_metal_ion_refined 0.205 r_chiral_restr 0.154 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 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 Atoms Number Protein Atoms 2349 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing