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Crystal Structure of Serine Palmitoyltransferase complexed with D-methylserine
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 293 PEG4000, Sodium acetate, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.27 45.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.843 α = 90 b = 61.843 β = 90 c = 208.344 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 1.7 50 97.5 0.999 20.5 10.1 44526
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 1.7 1.8 0.999
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 1.7 46.185 44523 4294 97.476 0.178 0.1733 0.1854 0.2186 0.2296 25.467
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] 1.059 1.059 -2.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.25 r_dihedral_angle_4_deg 18.184 r_dihedral_angle_3_deg 14.378 r_dihedral_angle_1_deg 6.466 r_lrange_it 5.352 r_lrange_other 5.351 r_scangle_it 4.248 r_scangle_other 4.247 r_scbond_it 2.853 r_scbond_other 2.852
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.25 r_dihedral_angle_4_deg 18.184 r_dihedral_angle_3_deg 14.378 r_dihedral_angle_1_deg 6.466 r_lrange_it 5.352 r_lrange_other 5.351 r_scangle_it 4.248 r_scangle_other 4.247 r_scbond_it 2.853 r_scbond_other 2.852 r_mcangle_other 2.619 r_mcangle_it 2.618 r_mcbond_other 2.008 r_mcbond_it 2.007 r_angle_refined_deg 1.706 r_angle_other_deg 1.423 r_nbd_refined 0.211 r_symmetry_nbd_other 0.174 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.167 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.153 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_symmetry_xyhbond_nbd_other 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3031 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing