☰ Navigation Tabs
Structure of the apo form of the N terminal domain of Bc2L-C lectin (1-131)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 5.5 mg/ml of protein, 1.2 M sodium citrate, at 292 K temperature and cryoprotected with 2.5 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 1.81 33.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.987 α = 90 b = 42.987 β = 90 c = 94.678 γ = 120
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 2020-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9801 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.5 19.97 99.9 0.083 0.085 0.021 0.999 21.7 16.4 15915
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 0.454 0.471 0.123 0.935 15.5
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 6tig 1.5 19.97 15120 762 99.92 0.1502 0.1488 0.1525 0.1778 0.1789 RANDOM 15.084
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] -2.99 -2.99 5.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.642 r_dihedral_angle_3_deg 11.043 r_dihedral_angle_4_deg 10.952 r_dihedral_angle_1_deg 7.871 r_angle_refined_deg 1.851 r_angle_other_deg 1.505 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.642 r_dihedral_angle_3_deg 11.043 r_dihedral_angle_4_deg 10.952 r_dihedral_angle_1_deg 7.871 r_angle_refined_deg 1.851 r_angle_other_deg 1.505 r_chiral_restr 0.086 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 949 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing