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rTBL Recombinant Lectin From Tepary Bean
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 15% Peg smear low 100mM Tris pH 7.5
PEG to 30% for cryoprotection
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.572 α = 96.352 b = 64.472 β = 101.952 c = 67.59 γ = 97.268
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 2018-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97918 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.9 32.732 99.7 0.073 0.088 0.049 0.997 11 6.2 73400
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 98.8 0.529 0.649 0.372 0.902 2.8 5.7
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 1fat 1.9 32.73 73390 3646 99.697 0.171 0.1692 0.1776 0.2132 0.2218 28.932
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] 1.385 -2.801 -2.541 0.265 0.713 -0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.062 r_dihedral_angle_4_deg 17.023 r_dihedral_angle_3_deg 14.13 r_dihedral_angle_1_deg 7.677 r_lrange_it 7.209 r_lrange_other 7.173 r_scangle_it 5.973 r_scangle_other 5.972 r_mcangle_other 4.471 r_mcangle_it 4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.062 r_dihedral_angle_4_deg 17.023 r_dihedral_angle_3_deg 14.13 r_dihedral_angle_1_deg 7.677 r_lrange_it 7.209 r_lrange_other 7.173 r_scangle_it 5.973 r_scangle_other 5.972 r_mcangle_other 4.471 r_mcangle_it 4.47 r_scbond_it 4.262 r_scbond_other 4.261 r_mcbond_it 3.439 r_mcbond_other 3.429 r_angle_refined_deg 1.846 r_angle_other_deg 1.445 r_symmetry_nbd_refined 0.257 r_nbd_other 0.243 r_symmetry_nbd_other 0.195 r_nbd_refined 0.19 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_other 0.142 r_symmetry_xyhbond_nbd_refined 0.114 r_metal_ion_refined 0.11 r_ncsr_local_group_5 0.093 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.089 r_ncsr_local_group_6 0.089 r_ncsr_local_group_1 0.086 r_ncsr_local_group_4 0.085 r_ncsr_local_group_2 0.078 r_ncsr_local_group_3 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7015 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 260
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing