☰ Navigation Tabs
Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-055
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.4M sodium malonate
Crystal Properties Matthews coefficient Solvent content 6.25 80.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.109 α = 90 b = 159.267 β = 90 c = 220.04 γ = 90
Symmetry Space Group P 2 21 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 PILATUS3 6M 2020-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9119 Diamond I04-1
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 3.626 129.07 100 1 3.9 6.5 36355
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 3.63 3.69 0.2
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 5LB5 3.626 129.017 36185 1808 99.59 0.334 0.3322 0.3311 0.3594 0.3571 125.931
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] 0.787 -0.234 -0.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.499 r_lrange_other 21.253 r_lrange_it 21.252 r_dihedral_angle_3_deg 17.312 r_mcangle_it 14.224 r_mcangle_other 14.223 r_dihedral_angle_4_deg 13.673 r_scangle_it 13.36 r_scangle_other 13.359 r_mcbond_other 8.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.499 r_lrange_other 21.253 r_lrange_it 21.252 r_dihedral_angle_3_deg 17.312 r_mcangle_it 14.224 r_mcangle_other 14.223 r_dihedral_angle_4_deg 13.673 r_scangle_it 13.36 r_scangle_other 13.359 r_mcbond_other 8.708 r_mcbond_it 8.707 r_scbond_it 7.957 r_scbond_other 7.956 r_dihedral_angle_1_deg 6.971 r_angle_refined_deg 1.375 r_angle_other_deg 1.186 r_symmetry_xyhbond_nbd_refined 0.394 r_nbd_other 0.227 r_nbd_refined 0.221 r_symmetry_nbd_other 0.206 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.159 r_symmetry_nbd_refined 0.141 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_2 0.066 r_ncsr_local_group_1 0.059 r_xyhbond_nbd_other 0.057 r_symmetry_xyhbond_nbd_other 0.054 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8640 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing