☰ Navigation Tabs
Serine Palmitoyltransferase from Sphingobacterium multivorum
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 2.24 45.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.612 α = 90 b = 61.612 β = 90 c = 208.349 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 CCD RAYONIX MX225-HS 2018-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.9 SPring-8 BL26B2
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 1.4 50 100 1 20.6 10.8 80227
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 1.4 1.48 0.848
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 1.4 43.604 80166 8179 99.973 0.172 0.1685 0.1691 0.2017 0.2023 21.099
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] 0.468 0.468 -0.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.929 r_dihedral_angle_3_deg 14.371 r_dihedral_angle_4_deg 11.422 r_dihedral_angle_1_deg 6.567 r_lrange_it 5.484 r_lrange_other 5.484 r_scangle_it 3.872 r_scangle_other 3.871 r_scbond_it 2.736 r_scbond_other 2.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.929 r_dihedral_angle_3_deg 14.371 r_dihedral_angle_4_deg 11.422 r_dihedral_angle_1_deg 6.567 r_lrange_it 5.484 r_lrange_other 5.484 r_scangle_it 3.872 r_scangle_other 3.871 r_scbond_it 2.736 r_scbond_other 2.736 r_mcangle_it 2.084 r_mcangle_other 2.084 r_angle_refined_deg 1.895 r_angle_other_deg 1.564 r_mcbond_it 1.548 r_mcbond_other 1.547 r_nbd_refined 0.228 r_symmetry_nbd_refined 0.196 r_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.181 r_symmetry_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.171 r_nbd_other 0.168 r_symmetry_xyhbond_nbd_other 0.112 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3050 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing