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Structure of ALAS bound to glycine 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, 25% v/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.672 α = 115.76 b = 112.518 β = 98.31 c = 117.388 γ = 91.49
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 2.487 48.912 98.4 0.177 0.988 6.27 3.6 93703 43.52
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 2.49 2.63 97.9 0.892 0.577 1.43 3.4
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 2.487 48.91 88660 5044 98.59 0.1698 0.16761 0.1763 0.2074 0.2124 RANDOM 48.209
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] -0.48 -0.51 -0.65 -0.23 -0.39 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.672 r_dihedral_angle_3_deg 15.699 r_dihedral_angle_1_deg 6.208 r_long_range_B_other 5.523 r_long_range_B_refined 5.522 r_scangle_other 3.607 r_mcangle_it 2.82 r_mcangle_other 2.82 r_scbond_it 2.349 r_scbond_other 2.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.672 r_dihedral_angle_3_deg 15.699 r_dihedral_angle_1_deg 6.208 r_long_range_B_other 5.523 r_long_range_B_refined 5.522 r_scangle_other 3.607 r_mcangle_it 2.82 r_mcangle_other 2.82 r_scbond_it 2.349 r_scbond_other 2.349 r_mcbond_it 1.807 r_mcbond_other 1.807 r_angle_refined_deg 1.286 r_angle_other_deg 0.447 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 21950 Nucleic Acid Atoms Solvent Atoms 630 Heterogen Atoms 161
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing