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Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to substrate sphingolipids at 2.60 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9DIE
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 3.4 63.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.789 α = 90 b = 105.854 β = 93.62 c = 109.108 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 2023-12-20 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) 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 2.6 24.41 99.8 0.4 0.941 4.1 9 28219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 100 1.17 0.49 1.9 7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.6 24.41 26690 1528 99.84 0.15231 0.14906 0.20889 0.2118 RANDOM 19.505
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] -0.35 -0.2 0.12 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.962 r_dihedral_angle_1_deg 7.621 r_long_range_B_refined 7.129 r_long_range_B_other 7.035 r_dihedral_angle_2_deg 7.011 r_scangle_other 5.21 r_scbond_it 3.128 r_scbond_other 3.128 r_mcangle_other 2.432 r_mcangle_it 2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.962 r_dihedral_angle_1_deg 7.621 r_long_range_B_refined 7.129 r_long_range_B_other 7.035 r_dihedral_angle_2_deg 7.011 r_scangle_other 5.21 r_scbond_it 3.128 r_scbond_other 3.128 r_mcangle_other 2.432 r_mcangle_it 2.43 r_angle_refined_deg 1.78 r_mcbond_it 1.471 r_mcbond_other 1.466 r_angle_other_deg 0.596 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4476 Nucleic Acid Atoms Solvent Atoms 687 Heterogen Atoms 260
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PROTEUM2 data reduction Aimless data scaling MOLREP phasing