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Crystal structure of Serine Acetyltransferase (SAT) from Planctomyces limnophilus in complex with its inhibitor (Cysteine)
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 6.5 278 0.02 M Magnesium chloride hexahydrate, 0.05 M PIPES pH7.5, 10% w/v 1,6-hexanediol, 0.001 M spermine
Crystal Properties Matthews coefficient Solvent content 2.5 51.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.749 α = 90 b = 88.8 β = 113.22 c = 101.4 γ = 90
Symmetry Space Group C 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 MAR scanner 345 mm plate 2021-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU R-AXIS 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 46.59 93.55 0.04985 0.995 10.26 2 36602 35.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.538 100 0.2263 0.907 2
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 2.45 46.59 36049 1709 93.777 0.241 0.2394 0.2393 0.2837 0.2838 35.37
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] 4.268 -3.304 -0.1 -0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.223 r_dihedral_angle_4_deg 19.037 r_dihedral_angle_3_deg 17.651 r_lrange_it 9.619 r_dihedral_angle_1_deg 7.17 r_scangle_it 6.428 r_mcangle_it 5.536 r_scbond_it 4.085 r_mcbond_it 3.412 r_angle_refined_deg 1.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.223 r_dihedral_angle_4_deg 19.037 r_dihedral_angle_3_deg 17.651 r_lrange_it 9.619 r_dihedral_angle_1_deg 7.17 r_scangle_it 6.428 r_mcangle_it 5.536 r_scbond_it 4.085 r_mcbond_it 3.412 r_angle_refined_deg 1.544 r_nbtor_refined 0.311 r_symmetry_nbd_refined 0.258 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.11 r_symmetry_xyhbond_nbd_refined 0.073 r_ncsr_local_group_3 0.067 r_ncsr_local_group_2 0.052 r_ncsr_local_group_1 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6925 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing