☰ Navigation Tabs
Crystal structure of fused YR, an asymmetric 4-OT trimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 fYR-4OT was crystallized in 1.5-2M (NH4)2SO4, 0.1M HEPES buffer (pH 7.2-8.0), and 2% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.38 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.09 α = 102.36 b = 49.409 β = 102.16 c = 49.324 γ = 102.11
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 2021-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.00 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.29 50 96 0.04 8 2 18084
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 96.2 0.274 0.376 0.256 0.886 2
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 2.29 46.51 16254 1828 94.62 0.27274 0.26929 0.262 0.30333 0.2932 RANDOM 68.836
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] -18.7 2.69 -3.47 25.36 4.87 -6.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.363 r_dihedral_angle_3_deg 20.932 r_long_range_B_other 17.578 r_long_range_B_refined 17.576 r_dihedral_angle_4_deg 15.488 r_mcangle_it 9.895 r_mcangle_other 9.892 r_scangle_other 9.829 r_dihedral_angle_1_deg 8.573 r_mcbond_other 7.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.363 r_dihedral_angle_3_deg 20.932 r_long_range_B_other 17.578 r_long_range_B_refined 17.576 r_dihedral_angle_4_deg 15.488 r_mcangle_it 9.895 r_mcangle_other 9.892 r_scangle_other 9.829 r_dihedral_angle_1_deg 8.573 r_mcbond_other 7.183 r_mcbond_it 7.181 r_scbond_it 6.861 r_scbond_other 6.858 r_angle_refined_deg 1.573 r_angle_other_deg 1.353 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 2520 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction REFMAC phasing