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Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Glycine
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 2.25 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.573 α = 90 b = 61.573 β = 90 c = 207.774 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 2019-03-20 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 1.45 50 100 0.999 22.8 9.6 72011
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 1.45 1.54 0.969
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 1.45 46.059 72008 7291 99.978 0.192 0.1882 0.1901 0.2289 0.2316 20.116
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] 0.695 0.695 -1.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.003 r_dihedral_angle_3_deg 14.407 r_dihedral_angle_4_deg 12.998 r_dihedral_angle_1_deg 6.451 r_lrange_it 5.249 r_lrange_other 5.248 r_scangle_it 4.141 r_scangle_other 4.14 r_scbond_it 2.734 r_scbond_other 2.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.003 r_dihedral_angle_3_deg 14.407 r_dihedral_angle_4_deg 12.998 r_dihedral_angle_1_deg 6.451 r_lrange_it 5.249 r_lrange_other 5.248 r_scangle_it 4.141 r_scangle_other 4.14 r_scbond_it 2.734 r_scbond_other 2.733 r_mcangle_it 2.176 r_mcangle_other 2.176 r_angle_refined_deg 1.894 r_mcbond_it 1.652 r_mcbond_other 1.652 r_angle_other_deg 1.532 r_nbd_refined 0.228 r_symmetry_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.18 r_nbd_other 0.172 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.167 r_symmetry_nbd_refined 0.117 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.013 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 415 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing