☰ Navigation Tabs
scFv 2D10 re-refined as a complex with trehalose replacing the original alpha-1,6-mannobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 MES 6.5, Magnesium sulphate (1.5 M), potassium sodium tartrate tetrahydrate (0.1M).
Crystal Properties Matthews coefficient Solvent content 2.72 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.093 α = 90 b = 81.093 β = 90 c = 74.388 γ = 120
Symmetry Space Group P 31 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 173.15 CCD MARMOSAIC 225 mm CCD 2014-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97856 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.549 50 99.4 39.67 5.5 41534
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 FOURIER SYNTHESIS THROUGHOUT 5I4F 1.55 35.11 37096 4100 99.43 0.15561 0.15284 0.1676 0.18039 0.193 RANDOM 26.12
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] 0.46 0.23 0.46 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.53 r_dihedral_angle_4_deg 13.792 r_dihedral_angle_3_deg 11.22 r_dihedral_angle_1_deg 9.22 r_long_range_B_refined 6.527 r_long_range_B_other 6.245 r_scangle_other 2.263 r_mcangle_it 1.766 r_mcangle_other 1.766 r_angle_refined_deg 1.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.53 r_dihedral_angle_4_deg 13.792 r_dihedral_angle_3_deg 11.22 r_dihedral_angle_1_deg 9.22 r_long_range_B_refined 6.527 r_long_range_B_other 6.245 r_scangle_other 2.263 r_mcangle_it 1.766 r_mcangle_other 1.766 r_angle_refined_deg 1.714 r_scbond_it 1.449 r_scbond_other 1.449 r_mcbond_it 1.047 r_mcbond_other 1.047 r_angle_other_deg 0.954 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1818 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-3000 refinement