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Crystal structure of thermostable dienelactone hydrolase. Monoclinic space group.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F67
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Sodium fluoride, 0.1 M Bis-Tris propane 8.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.474 α = 90 b = 142.669 β = 96.524 c = 74.887 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 PILATUS 2M 2022-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.97718 LNLS SIRIUS MANACA
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 1.53 74.402 92.3 0.121 0.137 0.062 0.997 6.6 4.7 137099
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 1.53 1.556 98.3 4.082 4.556 1.995 0.363 0.5 5
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 1.79 74.402 84616 4200 91.084 0.162 0.161 0.1714 0.1903 0.1992 26.075
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] 2.268 0.037 -1.918 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.05 r_dihedral_angle_3_deg 12.126 r_dihedral_angle_2_deg 6.122 r_lrange_it 5.992 r_lrange_other 5.89 r_dihedral_angle_1_deg 5.782 r_scangle_it 4.348 r_scangle_other 4.348 r_scbond_it 2.799 r_scbond_other 2.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.05 r_dihedral_angle_3_deg 12.126 r_dihedral_angle_2_deg 6.122 r_lrange_it 5.992 r_lrange_other 5.89 r_dihedral_angle_1_deg 5.782 r_scangle_it 4.348 r_scangle_other 4.348 r_scbond_it 2.799 r_scbond_other 2.799 r_mcangle_it 2.381 r_mcangle_other 2.381 r_mcbond_it 1.57 r_mcbond_other 1.57 r_angle_refined_deg 1.556 r_angle_other_deg 0.547 r_nbd_other 0.244 r_symmetry_nbd_refined 0.228 r_nbd_refined 0.212 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.173 r_xyhbond_nbd_refined 0.162 r_ncsr_local_group_1 0.083 r_ncsr_local_group_5 0.083 r_ncsr_local_group_6 0.083 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_2 0.08 r_chiral_restr 0.079 r_ncsr_local_group_4 0.074 r_ncsr_local_group_3 0.06 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7435 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing