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Crystal structure of a lactonase double mutant in complex with ligand N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2M Ammonium Sulfate, 0.085M Sodium Cacodylate pH 6.5, 25-28%(w/v) Polyethylene Glycol 8000, 15%(v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.65 53.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.319 α = 90 b = 110.52 β = 99.93 c = 127.779 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 CCD RAYONIX MX-300 2017-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.32 25 95 0.067 0.077 0.038 12.6 3.9 50048
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 2.32 2.4 96.6 0.486 0.561 0.276 0.803 3.8
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 5IE4 2.32 25 47531 2490 94.86 0.21236 0.20958 0.2175 0.26634 0.2683 RANDOM 48.23
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] -1.8 0.53 0.12 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.469 r_dihedral_angle_3_deg 21.143 r_dihedral_angle_4_deg 18.072 r_long_range_B_refined 10.616 r_long_range_B_other 10.615 r_mcangle_it 7.25 r_mcangle_other 7.25 r_scangle_other 7.086 r_dihedral_angle_1_deg 5.815 r_mcbond_it 5.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.469 r_dihedral_angle_3_deg 21.143 r_dihedral_angle_4_deg 18.072 r_long_range_B_refined 10.616 r_long_range_B_other 10.615 r_mcangle_it 7.25 r_mcangle_other 7.25 r_scangle_other 7.086 r_dihedral_angle_1_deg 5.815 r_mcbond_it 5.254 r_mcbond_other 5.251 r_scbond_it 5.22 r_scbond_other 5.219 r_angle_refined_deg 1.196 r_angle_other_deg 0.725 r_chiral_restr 0.077 r_gen_planes_refined 0.012 r_bond_refined_d 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 8174 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing