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Structure elucidation of truncated AMS3 lipase from an Antarctic Pseudomonas
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FDM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 0.1 M HEPES sodium pH 7.5, 0.8 M Potassium sodium tartrate tetrahydrate
Crystal Properties Matthews coefficient Solvent content 2.94 58.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.753 α = 90 b = 94.693 β = 90 c = 126.431 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU 2016-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.77 40 99.7 9.4 2.1 27263
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.77 2.82
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4FDM 2.77 40 25583 1391 98.98 0.22463 0.2217 0.2284 0.2771 0.279 RANDOM 27.183
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] 3.73 -1.92 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.751 r_dihedral_angle_3_deg 19.322 r_dihedral_angle_4_deg 18.906 r_dihedral_angle_1_deg 7.306 r_long_range_B_refined 4.51 r_long_range_B_other 4.51 r_mcangle_other 2.767 r_mcangle_it 2.766 r_scangle_other 2.704 r_angle_refined_deg 1.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.751 r_dihedral_angle_3_deg 19.322 r_dihedral_angle_4_deg 18.906 r_dihedral_angle_1_deg 7.306 r_long_range_B_refined 4.51 r_long_range_B_other 4.51 r_mcangle_other 2.767 r_mcangle_it 2.766 r_scangle_other 2.704 r_angle_refined_deg 1.689 r_mcbond_it 1.671 r_mcbond_other 1.63 r_scbond_it 1.592 r_scbond_other 1.592 r_angle_other_deg 1.098 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6042 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-3000 data processing HKL-3000 data scaling REFMAC phasing