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Crystal structures fluoroacetate dehalogenase D4B from Delftia acidovorans strain D4B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 14 mg/ml
25 %(w/v) Polyethylene glycol 3350, 0.2 M Ammonium acetate, 0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.936 α = 101.598 b = 83.778 β = 96.027 c = 84.917 γ = 94.673
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 EIGER X 16M 2022-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95374 Australian Synchrotron MX2
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 1.98 82.538 97.6 0.181 0.22 0.123 0.985 3 3 77693 26.22
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 1.98 2.016 97 1.315 1.63 0.948 0.31 0.5 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.98 39.41 1.96 77162 3777 96.99 0.2226 0.2213 0.2215 0.2477 0.248 30.11
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 14.4142 f_angle_d 0.8375 f_chiral_restr 0.0435 f_plane_restr 0.0156 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9393 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing