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Crystal structure of TPADO in a substrate-free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N0Q 3N0Q, 3EBY experimental model PDB 3EBY 3N0Q, 3EBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 12.5% MPD,
12.5% PEG 3350,
12.5% PEG 1000,
0.3 M sodium nitrate,
0.3 M sodium phosphate dibasic,
0.3 M ammonium sulfate,
0.1 M buffer Imidazole/MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.81 56.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.807 α = 90 b = 220.807 β = 90 c = 84.093 γ = 120
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 EIGER2 XE 16M 2021-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.281 110.404 94.3 0.239 0.053 0.998 11 21.1 68994
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.281 2.441 63.3 2.767 0.605 0.648 1.4
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3N0Q, 3EBY 2.281 191.224 68975 3391 64.739 0.181 0.1788 0.2249 0.2058 48.369
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] 0.224 0.112 0.224 -0.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.552 r_dihedral_angle_4_deg 17.384 r_dihedral_angle_3_deg 17.376 r_dihedral_angle_1_deg 7.805 r_lrange_other 6.532 r_lrange_it 6.53 r_scangle_it 4.692 r_scangle_other 4.69 r_mcangle_other 4.366 r_mcangle_it 4.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.552 r_dihedral_angle_4_deg 17.384 r_dihedral_angle_3_deg 17.376 r_dihedral_angle_1_deg 7.805 r_lrange_other 6.532 r_lrange_it 6.53 r_scangle_it 4.692 r_scangle_other 4.69 r_mcangle_other 4.366 r_mcangle_it 4.365 r_scbond_it 2.923 r_scbond_other 2.921 r_mcbond_it 2.785 r_mcbond_other 2.784 r_angle_refined_deg 1.712 r_angle_other_deg 1.312 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_other 0.202 r_nbd_refined 0.199 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.143 r_ncsr_local_group_2 0.103 r_ncsr_local_group_1 0.095 r_ncsr_local_group_4 0.092 r_ncsr_local_group_6 0.092 r_ncsr_local_group_3 0.09 r_metal_ion_refined 0.083 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_5 0.081 r_symmetry_xyhbond_nbd_other 0.077 r_chiral_restr 0.073 r_dihedral_angle_other_3_deg 0.014 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13651 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing