☰ Navigation Tabs
A genetically encoded sensor based on a bacterial DNA ligase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M MES pH 6.0; 20% PEG mono 2000
Crystal Properties Matthews coefficient Solvent content 2.57 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.48 α = 90 b = 92.48 β = 90 c = 74.29 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 1 2023-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.987 SSRF BL17U
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 3 30.29 99.9 0.13 0.136 0.031 0.999 25.3 19.2 7642
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.08 1.632 0.369 0.927
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 (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 3 30.29 7245 384 99.84 0.21706 0.2149 0.2273 0.2561 0.24 RANDOM 83.024
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] 2.84 1.42 2.84 -9.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.618 r_dihedral_angle_2_deg 9.548 r_dihedral_angle_1_deg 6.996 r_long_range_B_refined 4.149 r_long_range_B_other 4.149 r_mcangle_it 3.363 r_mcangle_other 3.362 r_scangle_other 3.137 r_mcbond_it 2.279 r_mcbond_other 2.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.618 r_dihedral_angle_2_deg 9.548 r_dihedral_angle_1_deg 6.996 r_long_range_B_refined 4.149 r_long_range_B_other 4.149 r_mcangle_it 3.363 r_mcangle_other 3.362 r_scangle_other 3.137 r_mcbond_it 2.279 r_mcbond_other 2.274 r_scbond_it 2.13 r_scbond_other 2.129 r_angle_refined_deg 1.184 r_angle_other_deg 0.521 r_chiral_restr 0.047 r_bond_other_d 0.023 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2529 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MoRDa phasing