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Evolution of Enzymatic Activity in the Tautomerase Superfamily: Mechanistic and Structural Consequences of the L8R Mutation in 4-Oxalocrotonate Tautomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BJP PDB entry 1BJP with coordinates for OXP removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 3 microlitres of protein (20 mg/mL solution in 10 mM Tris-Cl, pH 7.0) mixed with an equal volume of reservoir buffer [30% O-(2-aminopropyl)-O-(2-methoxyethyl)polypropylene glycol 500, 100 mM 2-(N-morpholino)ethanesulfonic acid, pH 6.5, and 50 mM CsCl]. The resulting mixture was allowed to equilibrate against 50 microlitres of reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.863 α = 90 b = 80.863 β = 90 c = 117.038 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 RIGAKU RAXIS HTC 2004-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.8 50 99.9 0.12 0.162 5.7 7.8 10782 10209 2 35.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 100 0.401 0.424 7.7
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-Factor (All) 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 PDB entry 1BJP with coordinates for OXP removed 2.8 34 10726 10209 514 99.97 0.23327 0.23327 0.22979 0.2283 0.30109 0.2918 RANDOM 25.763
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] 1.3 0.65 1.3 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.983 r_scangle_it 5.885 r_scbond_it 3.186 r_angle_refined_deg 2.357 r_mcangle_it 2.338 r_mcbond_it 1.257 r_xyhbond_nbd_refined 0.325 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.248 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.983 r_scangle_it 5.885 r_scbond_it 3.186 r_angle_refined_deg 2.357 r_mcangle_it 2.338 r_mcbond_it 1.257 r_xyhbond_nbd_refined 0.325 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.248 r_chiral_restr 0.115 r_symmetry_hbond_refined 0.096 r_bond_refined_d 0.024 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2769 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MOLREP phasing REFMAC refinement HKL-2000 data reduction