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Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-homoserine
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 297 PEG4000, sodium acetate, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.23 44.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.238 α = 90 b = 61.238 β = 90 c = 208.097 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 2020-12-23 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 1.55 50 98.3 0.997 13.6 8.3 57736
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 1.55 1.64 0.924
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 1.55 45.95 57730 5954 98.363 0.187 0.1826 0.1934 0.2233 0.2317 13.975
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] -0.342 -0.342 0.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.719 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_3_deg 14.37 r_dihedral_angle_1_deg 6.613 r_lrange_it 4.232 r_lrange_other 3.936 r_scangle_it 2.654 r_scangle_other 2.654 r_scbond_it 1.739 r_scbond_other 1.739
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.719 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_3_deg 14.37 r_dihedral_angle_1_deg 6.613 r_lrange_it 4.232 r_lrange_other 3.936 r_scangle_it 2.654 r_scangle_other 2.654 r_scbond_it 1.739 r_scbond_other 1.739 r_angle_refined_deg 1.698 r_mcangle_it 1.546 r_mcangle_other 1.546 r_angle_other_deg 1.482 r_mcbond_it 1.064 r_mcbond_other 1.064 r_nbd_refined 0.219 r_nbd_other 0.181 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.167 r_symmetry_nbd_refined 0.164 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 475 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing