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Wild type oxalyl-CoA synthetase Pcs60p
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.2 M LiCl, 0.1M Hepes pH 8.0, 10-16% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.029 α = 90 b = 93.724 β = 93.811 c = 356.488 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 2M 2016-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
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 2.87 29.985 99.2 0.99 8.6 1.9 163072
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 2.87 2.97 99.6 0.5 1.3
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 2.87 29.985 163027 8186 99.003 0.229 0.2274 0.2274 0.2497 0.2497 80.108
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] 1.818 -1.017 -1.195 -0.483
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.454 r_dihedral_angle_4_deg 20.115 r_dihedral_angle_3_deg 19.637 r_dihedral_angle_1_deg 7.651 r_lrange_it 5.439 r_mcangle_it 2.522 r_scangle_it 2.216 r_angle_refined_deg 1.75 r_mcbond_it 1.46 r_scbond_it 1.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.454 r_dihedral_angle_4_deg 20.115 r_dihedral_angle_3_deg 19.637 r_dihedral_angle_1_deg 7.651 r_lrange_it 5.439 r_mcangle_it 2.522 r_scangle_it 2.216 r_angle_refined_deg 1.75 r_mcbond_it 1.46 r_scbond_it 1.303 r_symmetry_nbd_refined 0.35 r_nbtor_refined 0.29 r_symmetry_xyhbond_nbd_refined 0.268 r_nbd_refined 0.172 r_chiral_restr 0.159 r_xyhbond_nbd_refined 0.107 r_ncsr_local_group_8 0.049 r_ncsr_local_group_27 0.049 r_ncsr_local_group_1 0.046 r_ncsr_local_group_12 0.046 r_ncsr_local_group_18 0.046 r_ncsr_local_group_22 0.046 r_ncsr_local_group_26 0.046 r_ncsr_local_group_35 0.046 r_ncsr_local_group_2 0.045 r_ncsr_local_group_7 0.045 r_ncsr_local_group_3 0.044 r_ncsr_local_group_16 0.044 r_ncsr_local_group_21 0.044 r_ncsr_local_group_24 0.044 r_ncsr_local_group_20 0.043 r_ncsr_local_group_29 0.043 r_ncsr_local_group_13 0.042 r_ncsr_local_group_28 0.041 r_ncsr_local_group_48 0.041 r_ncsr_local_group_9 0.04 r_ncsr_local_group_10 0.04 r_ncsr_local_group_11 0.04 r_ncsr_local_group_17 0.04 r_ncsr_local_group_25 0.04 r_ncsr_local_group_30 0.04 r_ncsr_local_group_63 0.04 r_ncsr_local_group_5 0.039 r_ncsr_local_group_15 0.039 r_ncsr_local_group_19 0.039 r_ncsr_local_group_23 0.039 r_ncsr_local_group_4 0.038 r_ncsr_local_group_36 0.038 r_ncsr_local_group_37 0.038 r_ncsr_local_group_38 0.038 r_ncsr_local_group_57 0.038 r_ncsr_local_group_59 0.038 r_ncsr_local_group_62 0.038 r_ncsr_local_group_32 0.037 r_ncsr_local_group_34 0.037 r_ncsr_local_group_52 0.037 r_ncsr_local_group_55 0.037 r_ncsr_local_group_58 0.037 r_ncsr_local_group_64 0.037 r_ncsr_local_group_66 0.037 r_ncsr_local_group_50 0.036 r_ncsr_local_group_61 0.036 r_ncsr_local_group_45 0.035 r_ncsr_local_group_54 0.035 r_ncsr_local_group_65 0.035 r_ncsr_local_group_6 0.034 r_ncsr_local_group_40 0.034 r_ncsr_local_group_41 0.034 r_ncsr_local_group_42 0.034 r_ncsr_local_group_60 0.034 r_ncsr_local_group_44 0.033 r_ncsr_local_group_53 0.033 r_ncsr_local_group_56 0.033 r_ncsr_local_group_14 0.032 r_ncsr_local_group_31 0.032 r_ncsr_local_group_47 0.032 r_ncsr_local_group_43 0.031 r_ncsr_local_group_51 0.031 r_ncsr_local_group_39 0.03 r_ncsr_local_group_46 0.03 r_ncsr_local_group_33 0.029 r_ncsr_local_group_49 0.029 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 42466 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing