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LecB in complex with photoswitchable compound GTB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.3 293 20% PEG 8K, 0.25M LiCl, 0.1M Sodium acetate pH 4.3
Crystal Properties Matthews coefficient Solvent content 2.29 46.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.21 α = 90 b = 83.72 β = 90 c = 158.88 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER2 XE 16M 2024-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 1.491 79.44 99.4 0.994 8 12.4 69682
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 1.491 1.516 0.319
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.491 79.44 69661 3512 99.404 0.151 0.1478 0.1577 0.2148 0.216 15.729
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] -1.093 -0.506 1.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.595 r_dihedral_angle_2_deg 14.269 r_dihedral_angle_3_deg 12.654 r_dihedral_angle_1_deg 7.296 r_scangle_it 7.124 r_scangle_other 7.122 r_lrange_it 6.689 r_lrange_other 6.528 r_rigid_bond_restr 6.053 r_scbond_it 5.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.595 r_dihedral_angle_2_deg 14.269 r_dihedral_angle_3_deg 12.654 r_dihedral_angle_1_deg 7.296 r_scangle_it 7.124 r_scangle_other 7.122 r_lrange_it 6.689 r_lrange_other 6.528 r_rigid_bond_restr 6.053 r_scbond_it 5.858 r_scbond_other 5.856 r_mcangle_it 3.194 r_mcangle_other 3.194 r_mcbond_it 2.805 r_mcbond_other 2.805 r_angle_refined_deg 1.721 r_angle_other_deg 0.585 r_nbd_other 0.283 r_symmetry_nbd_refined 0.255 r_nbd_refined 0.234 r_symmetry_nbd_other 0.205 r_xyhbond_nbd_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.165 r_symmetry_xyhbond_nbd_other 0.146 r_symmetry_nbtor_other 0.089 r_metal_ion_refined 0.089 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3282 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling REFMAC phasing