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Dienelactone hydrolase family protein m3DLH from Halieaceae bacterium
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 291 0.1 M Na3 Cit 5.6 pH (Buffer)
30 %w/v PEG 4K (Precipitant)
0.2 M NH4 Acet (Salt)
Crystal Properties Matthews coefficient Solvent content 1.94 36.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.445 α = 90 b = 43.68 β = 92.713 c = 59.645 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2019-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 24.27 98.36 0.1138 0.99 9.53 6.7 29979 15.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.58 0.5259 0.85 2.13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3f67 1.53 24.27 1.34 29949 1475 98.4 0.1657 0.1639 0.2014 0.2165 23.52
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 f_dihedral_angle_d 23.9601 f_angle_d 0.9748 f_chiral_restr 0.0582 f_bond_d 0.0082 f_plane_restr 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1850 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction Aimless data scaling PHENIX phasing