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Crystal structure of PbdA bound to p-methoxybenzoate.
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 = 52.17 α = 99.87 b = 55.11 β = 94.9 c = 64.26 γ = 103.24
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 2022-05-07 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) 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 2.03 52.595 97.92 0.1713 0.99 6.1 3.57 43063
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 2.03 2.07 96.46 1.553 0.95 0.304 0.75 3.6
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 2.03 52.595 43061 2174 97.915 0.169 0.1641 0.1751 0.2575 0.2601 23.606
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] 0.466 -1.038 -0.113 -0.509 -0.878 0.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.31 r_dihedral_angle_3_deg 14.933 r_lrange_it 14.786 r_lrange_other 14.482 r_dihedral_angle_2_deg 13.652 r_scangle_it 10.458 r_scangle_other 10.456 r_mcangle_it 10.27 r_mcangle_other 10.269 r_scbond_it 7.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.31 r_dihedral_angle_3_deg 14.933 r_lrange_it 14.786 r_lrange_other 14.482 r_dihedral_angle_2_deg 13.652 r_scangle_it 10.458 r_scangle_other 10.456 r_mcangle_it 10.27 r_mcangle_other 10.269 r_scbond_it 7.196 r_scbond_other 7.195 r_dihedral_angle_1_deg 7.09 r_mcbond_it 6.979 r_mcbond_other 6.979 r_rigid_bond_restr 4.986 r_angle_refined_deg 2.202 r_angle_other_deg 0.901 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.203 r_symmetry_nbd_refined 0.188 r_nbd_other 0.179 r_nbtor_refined 0.171 r_symmetry_nbd_other 0.164 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.113 r_ncsr_local_group_1 0.098 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.007 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6014 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing