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pro-concanavalin A: Precursor of circularly permuted concanavalin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 Zinc chloride, HEPES, PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.09 41.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.939 α = 90 b = 90.42 β = 91.128 c = 86.863 γ = 90
Symmetry Space Group I 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 EIGER X 16M 2019-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9536 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.1 48.885 98.8 0.994 6.5 3.4 26657
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.743
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1JBC 2.103 48.885 26647 1307 98.791 0.193 0.1908 0.1957 0.2441 0.2452 30.506
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] 1.672 1.335 -2.213 0.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.566 r_dihedral_angle_4_deg 19.784 r_dihedral_angle_3_deg 14.399 r_dihedral_angle_1_deg 8.915 r_lrange_it 6.111 r_lrange_other 6.109 r_scangle_it 4.152 r_scangle_other 4.152 r_mcangle_it 3.408 r_mcangle_other 3.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.566 r_dihedral_angle_4_deg 19.784 r_dihedral_angle_3_deg 14.399 r_dihedral_angle_1_deg 8.915 r_lrange_it 6.111 r_lrange_other 6.109 r_scangle_it 4.152 r_scangle_other 4.152 r_mcangle_it 3.408 r_mcangle_other 3.407 r_scbond_it 2.742 r_scbond_other 2.741 r_mcbond_it 2.23 r_mcbond_other 2.23 r_angle_refined_deg 1.527 r_angle_other_deg 1.245 r_symmetry_nbd_refined 0.305 r_symmetry_metal_ion_refined 0.262 r_nbd_other 0.255 r_symmetry_xyhbond_nbd_refined 0.237 r_nbd_refined 0.198 r_metal_ion_refined 0.191 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.126 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_symmetry_xyhbond_nbd_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3677 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building