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K352D oxalyl-CoA synthetase Pcs60p
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 Ammonium sulfate 0.15M, MES 0.1M pH6, PEG 4000 15%(w/v)
Crystal Properties Matthews coefficient Solvent content 2.49 50.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.931 α = 90 b = 125.6 β = 96.929 c = 80.495 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2020-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.987 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.45 47.092 99.9 0.991 5.1 4 43458
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.54 99.9 0.514 1.1 4.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold model 2.45 47.092 43433 2241 99.894 0.208 0.2057 0.2056 0.2473 0.2475 45.66
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] -0.434 -0.189 -1.158 1.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.708 r_dihedral_angle_3_deg 17.842 r_dihedral_angle_4_deg 16.93 r_dihedral_angle_1_deg 7.597 r_lrange_it 6.285 r_scangle_it 4.056 r_mcangle_it 3.563 r_scbond_it 2.609 r_mcbond_it 2.161 r_angle_refined_deg 1.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.708 r_dihedral_angle_3_deg 17.842 r_dihedral_angle_4_deg 16.93 r_dihedral_angle_1_deg 7.597 r_lrange_it 6.285 r_scangle_it 4.056 r_mcangle_it 3.563 r_scbond_it 2.609 r_mcbond_it 2.161 r_angle_refined_deg 1.828 r_nbtor_refined 0.291 r_nbd_refined 0.176 r_chiral_restr 0.164 r_symmetry_nbd_refined 0.164 r_xyhbond_nbd_refined 0.114 r_symmetry_xyhbond_nbd_refined 0.106 r_ncsr_local_group_1 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7192 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing