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Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Tris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG4000, sodium acetate, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.321 α = 90 b = 61.321 β = 90 c = 208.573 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 2019-09-09 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) 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 1.65 50 96.8 0.063 0.024 0.999 23.4 8.9 47616
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 0.222 0.128 0.956 6.4
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 3A2B 1.65 46.031 47601 4916 96.957 0.174 0.1695 0.2143 0.2242 15.038
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] -0.344 -0.344 0.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.688 r_dihedral_angle_4_deg 15.241 r_dihedral_angle_3_deg 14.164 r_dihedral_angle_1_deg 6.575 r_lrange_it 4.588 r_lrange_other 4.587 r_scangle_it 2.899 r_scangle_other 2.898 r_scbond_it 1.916 r_scbond_other 1.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.688 r_dihedral_angle_4_deg 15.241 r_dihedral_angle_3_deg 14.164 r_dihedral_angle_1_deg 6.575 r_lrange_it 4.588 r_lrange_other 4.587 r_scangle_it 2.899 r_scangle_other 2.898 r_scbond_it 1.916 r_scbond_other 1.916 r_angle_refined_deg 1.675 r_mcangle_it 1.662 r_mcangle_other 1.662 r_angle_other_deg 1.47 r_mcbond_it 1.125 r_mcbond_other 1.122 r_nbd_refined 0.218 r_nbd_other 0.194 r_xyhbond_nbd_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.185 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.165 r_symmetry_nbd_refined 0.161 r_symmetry_xyhbond_nbd_other 0.137 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.08 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 456 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing