☰ Navigation Tabs
Crystal structure of SxRhaGT in complex with TDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 2% v/v Polyethylene glycol 400, 0.1 M Imidazole pH7.0, 24% w/v PEG monomethyl ether 5,000
Crystal Properties Matthews coefficient Solvent content 2.28 46.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.39 α = 90 b = 91.98 β = 90 c = 102.5 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M 2024-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.61 68.53 99.8 0.182 0.195 0.067 7.2 12.9 104690
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 1.61 1.62 1.47
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 1.61 39.29 88527 4586 99.83 0.21762 0.21616 0.223 0.24547 0.2517 RANDOM 25.714
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] 1.41 -0.01 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.716 r_dihedral_angle_4_deg 16.026 r_dihedral_angle_3_deg 13.836 r_dihedral_angle_1_deg 5.326 r_long_range_B_refined 4.573 r_long_range_B_other 4.524 r_scangle_other 3.284 r_mcangle_it 2.37 r_mcangle_other 2.37 r_scbond_it 2.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.716 r_dihedral_angle_4_deg 16.026 r_dihedral_angle_3_deg 13.836 r_dihedral_angle_1_deg 5.326 r_long_range_B_refined 4.573 r_long_range_B_other 4.524 r_scangle_other 3.284 r_mcangle_it 2.37 r_mcangle_other 2.37 r_scbond_it 2.136 r_scbond_other 2.131 r_mcbond_it 1.596 r_mcbond_other 1.595 r_angle_refined_deg 1.531 r_angle_other_deg 0.825 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 5413 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data scaling HKL-3000 data reduction Coot model building PHASER phasing