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Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200 in complex with benzylamine
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 6.5 289 5 mg/ml SPL, 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.49 50.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.97 α = 90 b = 88.552 β = 96.17 c = 65.761 γ = 90
Symmetry Space Group P 1 21 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 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 1.5 36.66 98.9 0.105 0.125 0.066 0.995 11.5 6.8 110029
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 1.5 1.52 0.573 0.682 0.364 0.874 6.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 36.66 109867 5447 99.008 0.139 0.1376 0.1577 0.1721 15.039
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] 0.052 0.387 0.553 -0.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.77 r_dihedral_angle_3_deg 14.276 r_dihedral_angle_2_deg 7.677 r_lrange_it 6.311 r_dihedral_angle_1_deg 6.017 r_lrange_other 5.842 r_scangle_it 4.696 r_scangle_other 4.695 r_scbond_it 3.075 r_scbond_other 3.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.77 r_dihedral_angle_3_deg 14.276 r_dihedral_angle_2_deg 7.677 r_lrange_it 6.311 r_dihedral_angle_1_deg 6.017 r_lrange_other 5.842 r_scangle_it 4.696 r_scangle_other 4.695 r_scbond_it 3.075 r_scbond_other 3.075 r_mcangle_it 2.366 r_mcangle_other 2.365 r_angle_refined_deg 1.738 r_mcbond_it 1.633 r_mcbond_other 1.607 r_angle_other_deg 0.586 r_symmetry_xyhbond_nbd_refined 0.31 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.184 r_nbd_other 0.15 r_symmetry_nbd_refined 0.107 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_1 0.073 r_symmetry_xyhbond_nbd_other 0.06 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4674 Nucleic Acid Atoms Solvent Atoms 899 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing