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AAD-1 Bound to the Vanadyl Ion and Succinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 25% PEG 3350, 0.3 M Li2SO4, and 0.1 M bicine (pH 9.0). Ligands were soaked into crystals.
Crystal Properties Matthews coefficient Solvent content 2.21 44.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.915 α = 90 b = 97.868 β = 90 c = 69.855 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2018-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim 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 1.51 25 99.2 0.07 0.072 0.076 0.998 20.5 13.8 92316
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.54 99.4 0.792 8.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1GQW 1.51 25 87655 4573 99.18 0.19661 0.19554 0.1969 0.21739 0.2179 RANDOM 23.397
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] -0.5 0.84 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_3_deg 13.131 r_dihedral_angle_4_deg 11.158 r_dihedral_angle_1_deg 5.914 r_long_range_B_refined 4.552 r_mcangle_it 1.349 r_angle_refined_deg 1.16 r_scbond_it 0.828 r_mcbond_it 0.751 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_3_deg 13.131 r_dihedral_angle_4_deg 11.158 r_dihedral_angle_1_deg 5.914 r_long_range_B_refined 4.552 r_mcangle_it 1.349 r_angle_refined_deg 1.16 r_scbond_it 0.828 r_mcbond_it 0.751 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4415 Nucleic Acid Atoms Solvent Atoms 650 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHENIX phasing