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Crystal structure of PbdA bound to veratrate
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 7.5
Crystal Properties Matthews coefficient Solvent content 1.93 36.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.999 α = 98.676 b = 55.357 β = 95.002 c = 64.693 γ = 99.014
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 CdTe 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 1.85 63.54 97.6 0.129 0.182 0.129 0.99 4.8 3.2 57209
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) 1.85 1.89 95.9 1.109 1.568 1.109 0.412 0.9 3.5
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 1.85 63.54 57189 2837 97.491 0.21 0.2078 0.2109 0.258 0.262 24.936
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] -0.602 -0.588 0.907 0.832 0.348 -0.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.198 r_dihedral_angle_3_deg 14.68 r_dihedral_angle_2_deg 7.23 r_dihedral_angle_1_deg 7.142 r_lrange_it 5.09 r_lrange_other 4.923 r_scangle_it 3.549 r_scangle_other 3.549 r_mcangle_it 2.947 r_mcangle_other 2.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.198 r_dihedral_angle_3_deg 14.68 r_dihedral_angle_2_deg 7.23 r_dihedral_angle_1_deg 7.142 r_lrange_it 5.09 r_lrange_other 4.923 r_scangle_it 3.549 r_scangle_other 3.549 r_mcangle_it 2.947 r_mcangle_other 2.947 r_scbond_it 2.318 r_scbond_other 2.317 r_mcbond_it 2.032 r_mcbond_other 2.032 r_angle_refined_deg 1.697 r_angle_other_deg 0.599 r_xyhbond_nbd_refined 0.233 r_nbd_refined 0.224 r_symmetry_nbd_refined 0.22 r_symmetry_nbd_other 0.197 r_nbd_other 0.195 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.182 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.08 r_metal_ion_refined 0.06 r_symmetry_xyhbond_nbd_other 0.042 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6053 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing