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Rhombohedral crystalline form of human insulin complexed with m-cresol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 294.15 13.14 mg/mL human insulin, 0.80 mM zinc acetate, 0.51% v/v m-cresol in ethanol, 10.25 mM sodium thiocyanate, 0.4 M sodium-monopotassium phosphate mixture
Crystal Properties Matthews coefficient Solvent content 2.05 39.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.684 α = 90 b = 78.684 β = 90 c = 39.883 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2024-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.84 39.342 99.9 0.05 0.071 0.05 0.993 5.6 1.99 7990 36.419
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.88 99.6 0.408 0.577 0.408 0.627 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.84 39.342 7988 408 99.85 0.18 0.1779 0.1781 0.2239 0.2239 46.537
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] -0.113 -0.057 -0.113 0.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.045 r_dihedral_angle_6_deg 14.37 r_dihedral_angle_3_deg 13.333 r_lrange_it 8.103 r_lrange_other 8.067 r_scangle_it 6.794 r_scangle_other 6.788 r_dihedral_angle_1_deg 6.253 r_mcangle_other 5.102 r_mcangle_it 5.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.045 r_dihedral_angle_6_deg 14.37 r_dihedral_angle_3_deg 13.333 r_lrange_it 8.103 r_lrange_other 8.067 r_scangle_it 6.794 r_scangle_other 6.788 r_dihedral_angle_1_deg 6.253 r_mcangle_other 5.102 r_mcangle_it 5.092 r_scbond_other 4.948 r_scbond_it 4.947 r_mcbond_it 4.289 r_mcbond_other 4.284 r_angle_refined_deg 2.134 r_angle_other_deg 0.705 r_symmetry_xyhbond_nbd_refined 0.503 r_symmetry_nbd_refined 0.217 r_nbd_other 0.212 r_nbd_refined 0.21 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.194 r_xyhbond_nbd_refined 0.184 r_ncsr_local_group_1 0.142 r_ncsr_local_group_2 0.139 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.088 r_symmetry_metal_ion_refined 0.059 r_gen_planes_refined 0.014 r_bond_refined_d 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 748 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing