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Crystal structure of ScRhaGT in complex with TDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D0Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.5 50.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.959 α = 90 b = 110.572 β = 90 c = 157.026 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 2023-04-06 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) 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 1.73 43.26 99.9 0.8 8.4 11.9 82623 2
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 1.73 1.76 0.8
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 1.73 43.26 78342 4222 99.82 0.18586 0.18334 0.1964 0.23329 0.2456 RANDOM 35.139
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] 2.95 -0.52 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.715 r_dihedral_angle_4_deg 18.374 r_dihedral_angle_3_deg 13.665 r_long_range_B_refined 5.41 r_long_range_B_other 5.389 r_dihedral_angle_1_deg 5.336 r_mcangle_it 4.437 r_mcangle_other 4.437 r_scangle_other 4.43 r_scbond_it 3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.715 r_dihedral_angle_4_deg 18.374 r_dihedral_angle_3_deg 13.665 r_long_range_B_refined 5.41 r_long_range_B_other 5.389 r_dihedral_angle_1_deg 5.336 r_mcangle_it 4.437 r_mcangle_other 4.437 r_scangle_other 4.43 r_scbond_it 3.47 r_scbond_other 3.463 r_mcbond_it 3.405 r_mcbond_other 3.405 r_rigid_bond_restr 1.713 r_angle_refined_deg 1.451 r_angle_other_deg 0.831 r_chiral_restr 0.079 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5356 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement SCALA data scaling xia2 data reduction Coot model building PHASER phasing