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Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-048
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 2M ammonium sulfate -- 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.67 66.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.503 α = 90 b = 89.573 β = 90 c = 259.056 γ = 90
Symmetry Space Group P 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 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 2.74 129.63 99.6 1 4.8 6.6 49418
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 2.74 2.79 0.4
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 3.2 129.528 31267 1559 99.535 0.244 0.2419 0.2406 0.2746 0.271 69.309
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] -0.01 -0.037 0.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.083 r_dihedral_angle_3_deg 17.994 r_dihedral_angle_4_deg 16.607 r_lrange_other 12.142 r_lrange_it 12.141 r_mcangle_it 8.375 r_mcangle_other 8.374 r_scangle_other 8.245 r_scangle_it 8.239 r_dihedral_angle_1_deg 7.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.083 r_dihedral_angle_3_deg 17.994 r_dihedral_angle_4_deg 16.607 r_lrange_other 12.142 r_lrange_it 12.141 r_mcangle_it 8.375 r_mcangle_other 8.374 r_scangle_other 8.245 r_scangle_it 8.239 r_dihedral_angle_1_deg 7.333 r_mcbond_it 5.196 r_mcbond_other 5.195 r_scbond_other 4.988 r_scbond_it 4.985 r_angle_refined_deg 1.54 r_angle_other_deg 1.262 r_nbd_other 0.246 r_symmetry_xyhbond_nbd_refined 0.229 r_nbd_refined 0.213 r_symmetry_nbd_other 0.206 r_symmetry_nbd_refined 0.196 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.146 r_ncsr_local_group_1 0.089 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_2 0.069 r_chiral_restr 0.063 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8686 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing