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Crystal structure of serine palmitoyltransferase soaked in 190 mM D-serine solution
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 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.975 α = 90 b = 60.975 β = 90 c = 207.311 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 MX225HE 2017-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9 SPring-8 BL38B1
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 1.65 50 99.2 1 38.7 12.9 47801
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 1.65 1.75 0.991
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 1.651 42.248 47801 4946 99.15 0.152 0.1487 0.163 0.1842 0.1943 17.502
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] 0.618 0.618 -1.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.874 r_dihedral_angle_3_deg 14.889 r_dihedral_angle_1_deg 6.322 r_dihedral_angle_2_deg 6.237 r_lrange_it 5.286 r_lrange_other 5.286 r_scangle_it 4.003 r_scangle_other 4.002 r_scbond_it 2.687 r_scbond_other 2.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.874 r_dihedral_angle_3_deg 14.889 r_dihedral_angle_1_deg 6.322 r_dihedral_angle_2_deg 6.237 r_lrange_it 5.286 r_lrange_other 5.286 r_scangle_it 4.003 r_scangle_other 4.002 r_scbond_it 2.687 r_scbond_other 2.686 r_mcangle_it 2.117 r_mcangle_other 2.117 r_angle_refined_deg 1.682 r_mcbond_it 1.597 r_mcbond_other 1.597 r_angle_other_deg 0.569 r_nbd_refined 0.233 r_chiral_restr_other 0.222 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.163 r_nbd_other 0.162 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.131 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.016 r_xyhbond_nbd_other 0.011 r_bond_refined_d 0.01 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 407 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing