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Crystal structure of NaLdpA in complex with the product analog Resveratrol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2 M ammonium sulfate,
2% PEG 400,
0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.6 52.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.045 α = 90 b = 78.045 β = 90 c = 159.541 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 2020-09-23 M SINGLE WAVELENGTH 2 1 x-ray 45 PIXEL DECTRIS PILATUS 12M 2020-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03 2 SYNCHROTRON DIAMOND BEAMLINE I23 2.7552 Diamond I23
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 1.39 51.57 100 0.135 0.031 0.999 13.3 19.3 110449
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 1.39 1.41 99.7 2.756 0.826 0.35 0.4 11.8
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 SAD FREE R-VALUE 1.39 51.568 110151 5537 99.966 0.238 0.2372 0.2351 0.2588 0.2579 18.765
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] -0.099 -0.05 -0.099 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.099 r_dihedral_angle_4_deg 14.574 r_dihedral_angle_3_deg 13.656 r_dihedral_angle_1_deg 7.155 r_lrange_it 4.845 r_lrange_other 4.623 r_scangle_it 2.395 r_scangle_other 2.344 r_mcangle_it 1.875 r_mcangle_other 1.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.099 r_dihedral_angle_4_deg 14.574 r_dihedral_angle_3_deg 13.656 r_dihedral_angle_1_deg 7.155 r_lrange_it 4.845 r_lrange_other 4.623 r_scangle_it 2.395 r_scangle_other 2.344 r_mcangle_it 1.875 r_mcangle_other 1.875 r_angle_refined_deg 1.826 r_scbond_it 1.593 r_scbond_other 1.523 r_angle_other_deg 1.496 r_mcbond_it 1.222 r_mcbond_other 1.221 r_nbd_other 0.238 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.205 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_other 0.114 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_1 0.072 r_xyhbond_nbd_other 0.037 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3797 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling CRANK2 phasing