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Structure of THOUSAND-GRAIN WEIGHT 6 (TGW6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.6 283 0.8M sodium citrate tribasic, 0.1M CHES-NaOH, pH 9.6, 3% (w/v) sucrose
Crystal Properties Matthews coefficient Solvent content 3.26 62.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.982 α = 94.14 b = 108.52 β = 98.74 c = 123.071 γ = 97.23
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 EIGER X 4M 2020-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.999994 SPring-8 BL26B1
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 2.6 49.72 98.3 0.096 8.4 3.6 161474
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 2.6 2.64 0.736 1.4
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 2.6 48.99 153915 7877 98.26 0.22716 0.22545 0.2278 0.26025 0.2614 RANDOM 48.448
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] -1.07 -1.16 -0.4 0.82 0.63 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.193 r_dihedral_angle_4_deg 16.146 r_dihedral_angle_3_deg 14.915 r_dihedral_angle_1_deg 6.402 r_long_range_B_refined 3.642 r_long_range_B_other 3.642 r_mcangle_it 2.16 r_mcangle_other 2.16 r_scangle_other 1.762 r_mcbond_it 1.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.193 r_dihedral_angle_4_deg 16.146 r_dihedral_angle_3_deg 14.915 r_dihedral_angle_1_deg 6.402 r_long_range_B_refined 3.642 r_long_range_B_other 3.642 r_mcangle_it 2.16 r_mcangle_other 2.16 r_scangle_other 1.762 r_mcbond_it 1.207 r_mcbond_other 1.207 r_angle_refined_deg 1.202 r_angle_other_deg 1.035 r_scbond_it 0.966 r_scbond_other 0.966 r_chiral_restr 0.034 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 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 28704 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building BUCCANEER model building MOLREP phasing