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Crystal structure of a novel ZEN lactonase mutant with ligand Z
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2 M Ammonium Sulfate, 0.085 M Sodium Cacodylate pH 6.5, 25-28% w/v Polyethylene Glycol 8000 and 15% v/v Glycerol
Crystal Properties Matthews coefficient Solvent content 3.09 60.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.47 α = 90.21 b = 95.196 β = 92.34 c = 101.663 γ = 91.48
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 MX300-HS 2017-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.9998 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.88 25 97.8 0.058 7.9 4 224832
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.95 96.5 0.302 3.9
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 3WZL 1.88 24.95 222748 1999 97.72 0.14551 0.14519 0.1582 0.1811 0.1829 RANDOM 27.828
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.779 r_dihedral_angle_4_deg 12.775 r_dihedral_angle_3_deg 12.164 r_long_range_B_refined 7.131 r_long_range_B_other 7.071 r_dihedral_angle_1_deg 6.7 r_scangle_other 5.105 r_scbond_other 3.522 r_scbond_it 3.521 r_mcangle_other 3.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.779 r_dihedral_angle_4_deg 12.775 r_dihedral_angle_3_deg 12.164 r_long_range_B_refined 7.131 r_long_range_B_other 7.071 r_dihedral_angle_1_deg 6.7 r_scangle_other 5.105 r_scbond_other 3.522 r_scbond_it 3.521 r_mcangle_other 3.125 r_mcangle_it 3.124 r_mcbond_it 2.529 r_mcbond_other 2.527 r_angle_refined_deg 2.085 r_angle_other_deg 1.267 r_chiral_restr 0.132 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.004 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 16430 Nucleic Acid Atoms Solvent Atoms 2594 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing