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Crystal structure of BdThsB1 with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 283.15 10mg/ml protein, 160mM MgCl2, 100mM Tris pH7.5, 22.6% (w/v) PEG3350 (well)
1:1:0.2 protein/well/additive. the additive solution is 100mM Spermidine
Crystal Properties Matthews coefficient Solvent content 2.39 48.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.586 α = 90 b = 43.574 β = 90.031 c = 285.783 γ = 90
Symmetry Space Group P 1 21 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 9M 2025-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.539 50 99.7 0.07 0.038 0.997 23.09 5.78 159272
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 0.518 0.29 0.793 2.25
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 NONE 1.539 34.668 159254 7834 99.544 0.149 0.1472 0.1472 0.1828 0.1827 20.506
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] -0.015 -0.003 0.001 0.014
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.154 r_lrange_other 17.49 r_dihedral_angle_6_deg 16.079 r_dihedral_angle_3_deg 12.121 r_scangle_it 11.953 r_scangle_other 11.952 r_dihedral_angle_2_deg 10.675 r_mcangle_it 8.771 r_mcangle_other 8.771 r_scbond_it 8.412
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.154 r_lrange_other 17.49 r_dihedral_angle_6_deg 16.079 r_dihedral_angle_3_deg 12.121 r_scangle_it 11.953 r_scangle_other 11.952 r_dihedral_angle_2_deg 10.675 r_mcangle_it 8.771 r_mcangle_other 8.771 r_scbond_it 8.412 r_scbond_other 8.412 r_mcbond_it 6.09 r_mcbond_other 6.088 r_dihedral_angle_1_deg 5.448 r_rigid_bond_restr 4.579 r_dihedral_angle_other_2_deg 2.054 r_angle_refined_deg 1.66 r_angle_other_deg 1.098 r_chiral_restr_other 1.006 r_nbd_refined 0.241 r_symmetry_nbd_refined 0.223 r_symmetry_nbd_other 0.213 r_nbd_other 0.191 r_nbtor_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.183 r_xyhbond_nbd_refined 0.152 r_metal_ion_refined 0.119 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.034 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7328 Nucleic Acid Atoms Solvent Atoms 1010 Heterogen Atoms 284
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing