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Crystal structure of a novel ZEN lactonase mutant with ligand a
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 0.2M Ammonium Sulfate, 0.085M 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 60.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.462 α = 90.2 b = 95.158 β = 92.13 c = 101.444 γ = 91.6
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 97.6 0.08 6.8 3.9 222958
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 94.9 0.498 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WZL 1.88 24.93 220860 2038 97.5 0.156 0.156 0.195 0.1907 RANDOM 31.24
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 32.381 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_3_deg 12.63 r_long_range_B_refined 7.48 r_long_range_B_other 7.447 r_dihedral_angle_1_deg 6.698 r_scangle_other 5.548 r_scbond_it 3.698 r_scbond_other 3.698 r_mcangle_it 3.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.381 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_3_deg 12.63 r_long_range_B_refined 7.48 r_long_range_B_other 7.447 r_dihedral_angle_1_deg 6.698 r_scangle_other 5.548 r_scbond_it 3.698 r_scbond_other 3.698 r_mcangle_it 3.468 r_mcangle_other 3.467 r_mcbond_it 2.649 r_mcbond_other 2.647 r_angle_refined_deg 1.93 r_angle_other_deg 1.175 r_chiral_restr 0.123 r_bond_refined_d 0.02 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 16434 Nucleic Acid Atoms Solvent Atoms 2210 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing