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Crystal structure of TPADO in complex with TPA
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 2.82 56.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.714 α = 90 b = 219.714 β = 90 c = 82.964 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 2.078 190.278 96 0.167 0.037 0.999 14 21.3 111025
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 2.078 2.254 65.5 2.514 0.557 0.667 1.6 21.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3N0Q, 3EBY 2.08 190.278 111023 5502 80.98 0.17 0.1679 0.1646 0.214 0.2047 46.213
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] -0.038 -0.019 -0.038 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_4_deg 18.78 r_dihedral_angle_3_deg 15.199 r_dihedral_angle_1_deg 7.782 r_lrange_it 6.466 r_lrange_other 6.443 r_scangle_it 4.26 r_scangle_other 4.201 r_mcangle_it 3.194 r_mcangle_other 3.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_4_deg 18.78 r_dihedral_angle_3_deg 15.199 r_dihedral_angle_1_deg 7.782 r_lrange_it 6.466 r_lrange_other 6.443 r_scangle_it 4.26 r_scangle_other 4.201 r_mcangle_it 3.194 r_mcangle_other 3.194 r_scbond_it 2.988 r_scbond_other 2.94 r_mcbond_it 2.199 r_mcbond_other 2.198 r_angle_refined_deg 1.823 r_angle_other_deg 1.416 r_symmetry_nbd_refined 0.27 r_nbd_other 0.243 r_nbd_refined 0.201 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.151 r_ncsr_local_group_4 0.102 r_ncsr_local_group_6 0.1 r_ncsr_local_group_2 0.097 r_ncsr_local_group_1 0.089 r_ncsr_local_group_3 0.086 r_ncsr_local_group_5 0.085 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.083 r_symmetry_xyhbond_nbd_other 0.042 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13875 Nucleic Acid Atoms Solvent Atoms 953 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing