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Crystal structure of Serine Acetyltransferase (SAT) from Planctomyces limnophilus in complex with its substrate serine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 278 35% v/v 2-methyl-2,4-pentanediol, 100mM HEPES pH 7.5, 200mm NaCl
Crystal Properties Matthews coefficient Solvent content 2.65 53.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.98 α = 90 b = 90.03 β = 114.796 c = 122.544 γ = 90
Symmetry Space Group I 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 IMAGE PLATE RIGAKU 2020-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.218 40.858 93.25 0.06473 0.07397 0.03511 0.999 11.94 4.2 47993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.26 78.57 0.434 0.5074 0.847 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.218 40.858 47974 2329 93.273 0.216 0.2131 0.2156 0.2692 0.2735 58.739
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] 1.049 3.02 -0.723 -2.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.034 r_lrange_it 14.799 r_dihedral_angle_6_deg 14.261 r_scangle_it 11.316 r_mcangle_it 9.556 r_dihedral_angle_2_deg 8.976 r_scbond_it 7.955 r_dihedral_angle_1_deg 6.726 r_mcbond_it 6.68 r_angle_refined_deg 1.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.034 r_lrange_it 14.799 r_dihedral_angle_6_deg 14.261 r_scangle_it 11.316 r_mcangle_it 9.556 r_dihedral_angle_2_deg 8.976 r_scbond_it 7.955 r_dihedral_angle_1_deg 6.726 r_mcbond_it 6.68 r_angle_refined_deg 1.892 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.234 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.136 r_ncsr_local_group_3 0.082 r_ncsr_local_group_1 0.078 r_symmetry_xyhbond_nbd_refined 0.077 r_ncsr_local_group_2 0.072 r_bond_refined_d 0.008 r_metal_ion_refined 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6936 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing