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Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 1.85 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1 mg/mL protein, 0.4 mM ceramidephosphoethanolamine, 5 mg/mL CHAPS, 8.25% methyl-2,4-pentanediol, 75 mM sodium chloride, 27.5 mM sodium acetate (pH 4.6), ~30 mM Tris, 1 mM magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.33 63.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.999 α = 90 b = 105.327 β = 93.83 c = 108.406 γ = 90
Symmetry Space Group I 1 2 1
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 Bruker PHOTON III 2023-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 24.43 99.9 0.167 9.6 6.6 76317
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 1.836
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.85 24.43 72553 3751 99.9 0.12119 0.11878 0.1491 0.1674 0.1784 RANDOM 17.937
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] 0.08 -0.19 -0.14 0.08
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.166 r_long_range_B_other 18.143 r_dihedral_angle_3_deg 13.018 r_scangle_other 10.423 r_scbond_it 6.804 r_scbond_other 6.803 r_dihedral_angle_1_deg 6.704 r_dihedral_angle_2_deg 6.543 r_mcangle_other 5.305 r_mcangle_it 5.304
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.166 r_long_range_B_other 18.143 r_dihedral_angle_3_deg 13.018 r_scangle_other 10.423 r_scbond_it 6.804 r_scbond_other 6.803 r_dihedral_angle_1_deg 6.704 r_dihedral_angle_2_deg 6.543 r_mcangle_other 5.305 r_mcangle_it 5.304 r_mcbond_it 3.521 r_mcbond_other 3.517 r_rigid_bond_restr 3.376 r_angle_refined_deg 1.766 r_angle_other_deg 0.601 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4476 Nucleic Acid Atoms Solvent Atoms 884 Heterogen Atoms 254
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PROTEUM2 data reduction MOLREP phasing