☰ Navigation Tabs
Crystal structure of human RECQL5 helicase in complex with DSPL fragment(1-cyclohexyl-3-(oxolan-2-ylmethyl)urea, SGC - Diamond XChem I04-1 fragment screening.
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 0.1M tris pH 9.0 -- 29% PEG3350 -- 0.1M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.72 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.926 α = 109.9 b = 85.261 β = 90.02 c = 105.915 γ = 97.01
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 2016-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92820 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.47 79.49 92.3 0.097 5.8 2.5 69069
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.53 94.3 0.513 1.3 2.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5LB5 2.5 79.49 63558 3363 92.28 0.24 0.23665 0.2705 0.30292 0.3309 RANDOM 48.293
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] -0.92 -1.61 -0.7 1.47 1.54 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.668 r_dihedral_angle_4_deg 14.262 r_dihedral_angle_3_deg 14.231 r_long_range_B_refined 7.68 r_long_range_B_other 7.68 r_dihedral_angle_1_deg 7.675 r_mcangle_it 4.942 r_mcangle_other 4.941 r_scangle_other 4.831 r_mcbond_it 3.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.668 r_dihedral_angle_4_deg 14.262 r_dihedral_angle_3_deg 14.231 r_long_range_B_refined 7.68 r_long_range_B_other 7.68 r_dihedral_angle_1_deg 7.675 r_mcangle_it 4.942 r_mcangle_other 4.941 r_scangle_other 4.831 r_mcbond_it 3.062 r_mcbond_other 3.062 r_scbond_it 2.906 r_scbond_other 2.906 r_angle_refined_deg 1.496 r_angle_other_deg 0.958 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 13429 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing