☰ Navigation Tabs
Structure of legume lectin domain from Methanocaldococcus jannaschii in mannose bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BQP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1 M sodium acetate, pH 4.6 and 2 M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.03 α = 90 b = 55.03 β = 90 c = 149.05 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2018-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 1.75 51.624 100 0.99 9.4 7.4 24083
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 1.75 1.78 0.743 1.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2BQP 1.75 51.624 24000 1269 99.938 0.161 0.1594 0.1742 0.1828 0.1955 18.486
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] 0.469 0.469 -0.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.437 r_dihedral_angle_3_deg 12.382 r_dihedral_angle_1_deg 8.429 r_lrange_it 6.12 r_lrange_other 6.011 r_scangle_it 4.635 r_scangle_other 4.633 r_scbond_it 2.973 r_scbond_other 2.971 r_mcangle_it 2.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.437 r_dihedral_angle_3_deg 12.382 r_dihedral_angle_1_deg 8.429 r_lrange_it 6.12 r_lrange_other 6.011 r_scangle_it 4.635 r_scangle_other 4.633 r_scbond_it 2.973 r_scbond_other 2.971 r_mcangle_it 2.428 r_mcangle_other 2.258 r_angle_refined_deg 1.717 r_mcbond_it 1.704 r_angle_other_deg 1.505 r_mcbond_other 1.502 r_dihedral_angle_4_deg 0.423 r_symmetry_nbd_refined 0.24 r_nbd_refined 0.203 r_symmetry_nbd_other 0.2 r_nbd_other 0.185 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.165 r_symmetry_nbtor_other 0.101 r_metal_ion_refined 0.084 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1588 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing