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Y318A Human Aconitate Decarboxylase 1 mutant, apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 12UX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.8 295 100 mM Tris pH 8.8, 35% PEG 4000, 200 mM CaOAc, 200 nL drops, 2:1 protein:reservoir
Crystal Properties Matthews coefficient Solvent content 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.889 α = 90 b = 110.165 β = 90 c = 76.11 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 PIXEL DECTRIS EIGER X 9M 2025-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92021 NSLS-II 17-ID-1
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 1.62 34.55 94.4 0.136 0.28 0.072 0.995 8.4 13.9 80794 19.2
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 1.62 1.82 46.3 2.35 2.52 0.664 0.55 1.5 14.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.62 34.55 80793 4198 74.036 0.163 0.1604 0.1603 0.2019 0.2019 RANDOM 19.536
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] -0.316 0.262 0.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.817 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_2_deg 8.92 r_dihedral_angle_1_deg 6.402 r_lrange_it 4.829 r_lrange_other 4.666 r_scangle_it 2.349 r_scangle_other 2.348 r_mcangle_it 1.634 r_mcangle_other 1.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.817 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_2_deg 8.92 r_dihedral_angle_1_deg 6.402 r_lrange_it 4.829 r_lrange_other 4.666 r_scangle_it 2.349 r_scangle_other 2.348 r_mcangle_it 1.634 r_mcangle_other 1.634 r_angle_refined_deg 1.538 r_scbond_it 1.436 r_scbond_other 1.435 r_mcbond_it 0.974 r_mcbond_other 0.973 r_angle_other_deg 0.538 r_symmetry_metal_ion_refined 0.254 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.217 r_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.173 r_metal_ion_refined 0.166 r_nbd_other 0.161 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7084 Nucleic Acid Atoms Solvent Atoms 837 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing