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Crystal structure of PbdA bound to p-ethylbenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DNJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.8 M sodium phosphate, 0.8 M potassium phosphate, 0.1 M HEPES pH 7.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.751 α = 99.541 b = 54.437 β = 95.379 c = 64.018 γ = 102.644
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 2021-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.65 52.13 96.9 0.091 0.129 0.091 0.976 6 3.1 77677
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.65 1.68 95.2 1.614 2.283 1.614 0.345 0.7 3.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 52.13 77592 3907 96.784 0.197 0.1941 0.201 0.2467 0.2522 25.693
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] 1.836 -1.113 2.234 -1.405 -1.172 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.492 r_dihedral_angle_3_deg 13.32 r_dihedral_angle_2_deg 10.233 r_dihedral_angle_1_deg 6.876 r_lrange_it 5.729 r_lrange_other 5.671 r_scangle_it 4.423 r_scangle_other 4.422 r_mcangle_it 3.136 r_mcangle_other 3.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.492 r_dihedral_angle_3_deg 13.32 r_dihedral_angle_2_deg 10.233 r_dihedral_angle_1_deg 6.876 r_lrange_it 5.729 r_lrange_other 5.671 r_scangle_it 4.423 r_scangle_other 4.422 r_mcangle_it 3.136 r_mcangle_other 3.136 r_scbond_it 2.896 r_scbond_other 2.896 r_mcbond_it 2.203 r_mcbond_other 2.203 r_angle_refined_deg 1.705 r_angle_other_deg 0.608 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.203 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.181 r_nbd_other 0.176 r_metal_ion_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.139 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6047 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing