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Structure of ALAS bound to succinyl-CoA from S. cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.15 M magnesium chloride, 0.1 M HEPES, pH 7.5, 22.5% v/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.595 α = 116.403 b = 114.241 β = 97.507 c = 119.307 γ = 91.839
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 2023-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920105 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.69 48.77 98.5 0.235 0.978 5.3 3.6 77425 37.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.84 98 1.151 0.507 1.22 3.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.691 48.769 77425 3847 98.673 0.182 0.1801 0.186 0.2267 0.231 RANDOM 50.143
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] 0.965 -0.043 -0.133 0.669 -0.007 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.281 r_dihedral_angle_6_deg 13.87 r_dihedral_angle_2_deg 12.339 r_lrange_it 5.994 r_lrange_other 5.98 r_dihedral_angle_1_deg 5.896 r_scangle_it 4.512 r_scangle_other 4.512 r_scbond_it 2.897 r_scbond_other 2.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.281 r_dihedral_angle_6_deg 13.87 r_dihedral_angle_2_deg 12.339 r_lrange_it 5.994 r_lrange_other 5.98 r_dihedral_angle_1_deg 5.896 r_scangle_it 4.512 r_scangle_other 4.512 r_scbond_it 2.897 r_scbond_other 2.881 r_mcangle_it 2.82 r_mcangle_other 2.82 r_mcbond_it 1.761 r_mcbond_other 1.76 r_angle_refined_deg 1.393 r_angle_other_deg 0.489 r_dihedral_angle_other_2_deg 0.301 r_nbd_other 0.271 r_symmetry_nbd_refined 0.209 r_nbd_refined 0.204 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.173 r_symmetry_nbtor_other 0.077 r_ncsr_local_group_1 0.072 r_ncsr_local_group_3 0.069 r_ncsr_local_group_4 0.069 r_ncsr_local_group_6 0.068 r_ncsr_local_group_10 0.067 r_ncsr_local_group_2 0.066 r_symmetry_xyhbond_nbd_refined 0.065 r_chiral_restr 0.064 r_ncsr_local_group_5 0.064 r_ncsr_local_group_7 0.064 r_ncsr_local_group_8 0.064 r_ncsr_local_group_9 0.064 r_ncsr_local_group_12 0.062 r_ncsr_local_group_13 0.062 r_ncsr_local_group_14 0.062 r_ncsr_local_group_11 0.059 r_ncsr_local_group_15 0.059 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22230 Nucleic Acid Atoms Solvent Atoms 629 Heterogen Atoms 356
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing