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Crystal structure of Drosophila neural ectodermal development factor Imp-L1 with Human IGF-I
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 7.5 291 cp 10 mg/ml, 4-8% w/v PEG 6K, 5-20 mM MgCl2, 5 mM SB12, 0.1 M TRIS pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.03 α = 90 b = 94.15 β = 95.26 c = 48.36 γ = 90
Symmetry Space Group C 1 2 1
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 2013-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.57 48.16 96.4 0.093 0.059 3.9 3.9 10666
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 2.57 2.64 97.6 0.783 0.47 4.1
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 2.57 48.16 10666 535 95.65 0.23199 0.22938 0.2295 0.2852 0.2819 RANDOM 58.991
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] 3.14 0.3 -3.46 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.586 r_dihedral_angle_3_deg 24.866 r_dihedral_angle_4_deg 24.169 r_long_range_B_refined 11.001 r_long_range_B_other 11 r_scangle_other 7.04 r_dihedral_angle_1_deg 6.638 r_mcangle_it 6.208 r_mcangle_other 6.207 r_scbond_it 4.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.586 r_dihedral_angle_3_deg 24.866 r_dihedral_angle_4_deg 24.169 r_long_range_B_refined 11.001 r_long_range_B_other 11 r_scangle_other 7.04 r_dihedral_angle_1_deg 6.638 r_mcangle_it 6.208 r_mcangle_other 6.207 r_scbond_it 4.536 r_scbond_other 4.536 r_mcbond_it 4.107 r_mcbond_other 4.089 r_angle_refined_deg 1.676 r_angle_other_deg 0.835 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1886 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing