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Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200 in complex with N-benzyl-picolinamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 5 mg/ml SPL, 0.02 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 22% w/v Poly(acrylic acid sodium salt) 5,100
Crystal Properties Matthews coefficient Solvent content 2.84 56.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.833 α = 90 b = 60.833 β = 90 c = 217.692 γ = 90
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 EIGER2 X 16M 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033190 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 46.62 100 0.142 0.154 0.06 0.996 11.3 12.6 72849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 0.743 0.817 0.336 0.835 11.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 46.618 72765 3612 99.977 0.191 0.1886 0.1886 0.2277 0.2276 24.376
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] -0.177 -0.177 0.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.899 r_dihedral_angle_3_deg 15.082 r_dihedral_angle_2_deg 7.647 r_lrange_it 6.721 r_lrange_other 6.619 r_dihedral_angle_1_deg 6.422 r_scangle_it 6.06 r_scangle_other 6.059 r_scbond_it 4.318 r_scbond_other 4.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.899 r_dihedral_angle_3_deg 15.082 r_dihedral_angle_2_deg 7.647 r_lrange_it 6.721 r_lrange_other 6.619 r_dihedral_angle_1_deg 6.422 r_scangle_it 6.06 r_scangle_other 6.059 r_scbond_it 4.318 r_scbond_other 4.317 r_mcangle_it 3.626 r_mcangle_other 3.625 r_mcbond_it 2.976 r_mcbond_other 2.973 r_angle_refined_deg 1.84 r_angle_other_deg 1.037 r_symmetry_nbd_refined 0.581 r_nbd_other 0.242 r_nbd_refined 0.21 r_symmetry_nbd_other 0.21 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.147 r_symmetry_xyhbond_nbd_refined 0.139 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.088 r_ncsr_local_group_1 0.065 r_gen_planes_other 0.021 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4674 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction