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Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-alanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A2B 3A2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG4000, sodium acetate, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.23 44.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.234 α = 90 b = 61.234 β = 90 c = 208.182 γ = 90
Symmetry Space Group P 41 21 2
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 VII 2021-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.54 50 98.3 0.999 27.1 17.8 58899
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.63 0.965
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3A2B 1.54 45.956 58868 5972 98.39 0.177 0.1722 0.1835 0.2164 0.2245 16.383
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] 0.012 0.012 -0.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.483 r_dihedral_angle_4_deg 17.791 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_1_deg 6.492 r_lrange_it 4.993 r_lrange_other 4.992 r_scangle_it 3.314 r_scangle_other 3.313 r_scbond_it 2.155 r_scbond_other 2.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.483 r_dihedral_angle_4_deg 17.791 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_1_deg 6.492 r_lrange_it 4.993 r_lrange_other 4.992 r_scangle_it 3.314 r_scangle_other 3.313 r_scbond_it 2.155 r_scbond_other 2.155 r_mcangle_other 1.828 r_mcangle_it 1.827 r_angle_refined_deg 1.769 r_angle_other_deg 1.524 r_mcbond_it 1.266 r_mcbond_other 1.264 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.178 r_symmetry_nbd_other 0.176 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.169 r_symmetry_nbd_refined 0.147 r_symmetry_xyhbond_nbd_other 0.095 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3035 Nucleic Acid Atoms Solvent Atoms 493 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing