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Crystal structure of Drosophila neural ectodermal development factor Imp-L2 with Drosophila DILP5 insulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CBP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 Cp 10 mg/ml, 8-10% w/v PEG 4k or 6K, 20 mM MgCl2, 0.1 M HEPES pH 6.8-7.5
Crystal Properties Matthews coefficient Solvent content 3.71 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.834 α = 90 b = 150.834 β = 90 c = 125.321 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS3 S 6M 2012-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.91500 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.48 29.6 98.8 0.165 0.089 8 4.3 17857
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.48 3.67 1.17 0.63 4.3
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 4CBP 3.48 29.6 17857 971 98.76 0.26548 0.26141 0.2614 0.34456 0.3445 RANDOM 92.659
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] 0.97 0.97 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.844 r_dihedral_angle_3_deg 26.139 r_dihedral_angle_4_deg 20.811 r_long_range_B_refined 17.092 r_mcangle_it 10.351 r_dihedral_angle_1_deg 7.533 r_mcbond_it 6.335 r_scbond_it 6.252 r_angle_refined_deg 1.734 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.844 r_dihedral_angle_3_deg 26.139 r_dihedral_angle_4_deg 20.811 r_long_range_B_refined 17.092 r_mcangle_it 10.351 r_dihedral_angle_1_deg 7.533 r_mcbond_it 6.335 r_scbond_it 6.252 r_angle_refined_deg 1.734 r_chiral_restr 0.116 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5819 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing