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Crystal structure of Serine Acetyltransferase from Planctomyces limnophilus at 2.15A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 278 0.1M MES pH=6.5, 12% w/v PEG 20,000
Crystal Properties Matthews coefficient Solvent content 2.71 54.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.719 α = 90 b = 113.165 β = 90 c = 230.133 γ = 90
Symmetry Space Group P 21 21 21
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 RAXIS 2017-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5417
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 2.15 47.596 99.64 0.09531 0.1078 0.04956 0.997 14.44 4.7 120745 32.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.227 99.23 0.742 0.8414 0.3909 0.658 4.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3F1X 2.15 47.596 120491 1990 99.694 0.187 0.1866 0.223 0.1973 38.87
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] 1.514 0.095 -1.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.367 r_dihedral_angle_4_deg 18.619 r_dihedral_angle_3_deg 14.521 r_lrange_it 9.109 r_dihedral_angle_1_deg 6.52 r_scangle_it 6.248 r_mcangle_it 4.636 r_scbond_it 4.391 r_mcbond_it 3.148 r_angle_refined_deg 1.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.367 r_dihedral_angle_4_deg 18.619 r_dihedral_angle_3_deg 14.521 r_lrange_it 9.109 r_dihedral_angle_1_deg 6.52 r_scangle_it 6.248 r_mcangle_it 4.636 r_scbond_it 4.391 r_mcbond_it 3.148 r_angle_refined_deg 1.475 r_nbtor_refined 0.309 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.15 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.107 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14076 Nucleic Acid Atoms Solvent Atoms 766 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing