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DaCS-oxaloacetate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 0.2 M KCl, 0.05 M HEPES pH 7.5, 35% v/v Pentaerythritol propoxylate (5/4 PO/OH)
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.1 α = 90 b = 111.28 β = 116.07 c = 99.56 γ = 90
Symmetry Space Group C 1 2 1
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 4M 2022-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.46 45.11 98.98 0.182 0.255 0.981 6.7 3.3 54679
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 2.46 2.52 99.1 1.366 0.985 0.311 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 (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 2.46 45.11 51987 2662 98.98 0.21335 0.21109 0.2175 0.25756 0.2558 RANDOM 59.334
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] -0.11 -0.05 -0.24 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.462 r_dihedral_angle_3_deg 17.772 r_long_range_B_refined 11.477 r_long_range_B_other 11.477 r_scangle_other 8.946 r_mcangle_it 7.729 r_mcangle_other 7.729 r_dihedral_angle_1_deg 6.976 r_scbond_it 5.78 r_scbond_other 5.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.462 r_dihedral_angle_3_deg 17.772 r_long_range_B_refined 11.477 r_long_range_B_other 11.477 r_scangle_other 8.946 r_mcangle_it 7.729 r_mcangle_other 7.729 r_dihedral_angle_1_deg 6.976 r_scbond_it 5.78 r_scbond_other 5.779 r_mcbond_it 5.214 r_mcbond_other 5.212 r_angle_refined_deg 1.47 r_angle_other_deg 0.459 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10275 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing