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Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-serine
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 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.282 α = 90 b = 61.282 β = 90 c = 207.788 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 PIXEL DECTRIS EIGER X 16M 2019-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 1.5 50 99.8 0.998 15 9.3 64186
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 1.5 1.59 0.949
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 1.5 45.94 64160 6591 99.2 0.151 0.148 0.1479 0.184 0.184 19.881
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] 0.26 0.26 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.087 r_dihedral_angle_4_deg 16.641 r_dihedral_angle_3_deg 14.265 r_dihedral_angle_1_deg 6.238 r_lrange_it 5.281 r_lrange_other 5.024 r_scangle_it 3.859 r_scangle_other 3.859 r_scbond_it 2.579 r_scbond_other 2.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.087 r_dihedral_angle_4_deg 16.641 r_dihedral_angle_3_deg 14.265 r_dihedral_angle_1_deg 6.238 r_lrange_it 5.281 r_lrange_other 5.024 r_scangle_it 3.859 r_scangle_other 3.859 r_scbond_it 2.579 r_scbond_other 2.579 r_mcangle_it 2.009 r_mcangle_other 2.009 r_angle_refined_deg 1.829 r_angle_other_deg 1.572 r_mcbond_it 1.473 r_mcbond_other 1.473 r_chiral_restr_other 0.257 r_nbd_refined 0.222 r_symmetry_nbd_other 0.179 r_xyhbond_nbd_refined 0.176 r_nbd_other 0.176 r_symmetry_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.171 r_symmetry_nbd_refined 0.137 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_xyhbond_nbd_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 502 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing