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Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model RoseTTAFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 5 mg/ml SPL, Index screen condition 78 (0.2 M Ammonium acetate, 0.1 M BIS-TRIS, 25% PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.812 α = 90 b = 88.966 β = 96.411 c = 65.627 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 2021-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033210 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 1.99 42.05 94.9 0.071 0.099 0.068 0.992 9.5 3.4 44854
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 1.99 2.05 0.281 0.392 0.273 0.925 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.994 42.048 44805 2309 94.571 0.167 0.1647 0.1647 0.2017 0.2017 30.462
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] -1.029 0.507 1.902 -0.962
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.943 r_dihedral_angle_3_deg 15.415 r_lrange_it 9.53 r_lrange_other 9.493 r_scangle_it 8.644 r_scangle_other 8.643 r_dihedral_angle_2_deg 8.198 r_dihedral_angle_1_deg 6.966 r_scbond_it 6.051 r_scbond_other 6.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.943 r_dihedral_angle_3_deg 15.415 r_lrange_it 9.53 r_lrange_other 9.493 r_scangle_it 8.644 r_scangle_other 8.643 r_dihedral_angle_2_deg 8.198 r_dihedral_angle_1_deg 6.966 r_scbond_it 6.051 r_scbond_other 6.05 r_mcangle_other 4.705 r_mcangle_it 4.704 r_mcbond_it 3.776 r_mcbond_other 3.76 r_angle_refined_deg 2.037 r_angle_other_deg 0.641 r_nbd_refined 0.214 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.162 r_nbd_other 0.138 r_chiral_restr 0.106 r_ncsr_local_group_1 0.088 r_symmetry_nbtor_other 0.085 r_symmetry_nbd_refined 0.057 r_symmetry_xyhbond_nbd_other 0.021 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 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 360 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing