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WT Human Aconitate Decarboxylase 1, apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 100 mM Tris pH 8.0, 25% PEG 4000, 200 mM CaOAc, 200 nL drop, 2:1 protein:reservoir
Crystal Properties Matthews coefficient Solvent content 2.09 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.678 α = 90 b = 110.021 β = 90 c = 75.755 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 2025-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92 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 1.32 33.78 94.1 0.204 0.22 0.057 0.998 9.8 13.7 146042 11.4
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 1.32 1.49 55.6 2.5 2.742 0.789 0.331 1 11.6
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 1.32 33.78 146042 7369 74.009 0.16 0.1582 0.1582 0.1925 0.1926 17.596
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] 0.025 -0.232 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.977 r_dihedral_angle_3_deg 13.631 r_dihedral_angle_2_deg 8.39 r_lrange_it 6.224 r_dihedral_angle_1_deg 6.04 r_lrange_other 5.982 r_scangle_it 3.54 r_scangle_other 3.54 r_scbond_it 2.214 r_scbond_other 2.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.977 r_dihedral_angle_3_deg 13.631 r_dihedral_angle_2_deg 8.39 r_lrange_it 6.224 r_dihedral_angle_1_deg 6.04 r_lrange_other 5.982 r_scangle_it 3.54 r_scangle_other 3.54 r_scbond_it 2.214 r_scbond_other 2.213 r_mcangle_other 2.008 r_mcangle_it 2.007 r_angle_refined_deg 1.798 r_mcbond_it 1.254 r_mcbond_other 1.253 r_symmetry_metal_ion_refined 0.757 r_angle_other_deg 0.6 r_nbd_other 0.239 r_symmetry_nbd_refined 0.236 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.187 r_metal_ion_refined 0.152 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7109 Nucleic Acid Atoms Solvent Atoms 1004 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing