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The X-ray structure of the cis-3-chloroacrylic acid dehalogenase cis-CaaD inactivated with (R)-Oxirane-2-carboxylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S0Y trans-3-chloroacrylic acid dehalogenase (CaaD, PDB ID: 1S0Y)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 equal amounts of protein solution (10 mg/mL) and well solution containing 1.6 M potassium sodium phosphate and 100 mM HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.78 30.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.457 α = 90 b = 59.457 β = 90 c = 57.909 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MACSCIENCE mirrors 2004-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 30 100 0.103 19.8 6850 6850 2 2 5.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 100 0.355 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 trans-3-chloroacrylic acid dehalogenase (CaaD, PDB ID: 1S0Y) 2.1 28.96 6850 6850 327 99.9 0.204 0.1988 0.226 0.2266 RANDOM 16
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] 1.54 2.85 1.54 -3.08
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_scangle_it 2.68 c_scbond_it 1.79 c_mcangle_it 1.69 c_mcbond_it 1.41 c_angle_deg 1.3 c_improper_angle_d 0.64 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 890 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 6
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing