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Crystal structure of fluoroacetate dehalogenase 4A 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 293 8 mg/ml A4,
2 M Ammonium sulfate, 2% (v/v) PEG400,
0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.97 37.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.225 α = 90 b = 68.496 β = 90 c = 69.909 γ = 90
Symmetry Space Group P 21 21 21
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) 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 1.585 48.926 94.2 0.052 0.998 7.8 8.1 27201
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.585 1.612 1.748 0.528 0.4
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 (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 1.585 48.93 26822 1349 92.9 0.2266 0.2256 0.2175 0.2487 0.2375 RANDOM 27.37
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] 8.827 1.9322 -10.7592
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.43 t_omega_torsion 4.05 t_angle_deg 1 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1612 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 6
Software Software Software Name Purpose BUSTER refinement autoPROC data processing Aimless data scaling PHASER phasing XDS data reduction