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Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 25% PEG 3350, 0.1 M Bis Tris pH 6.5, 0.1 M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.249 α = 90 b = 83.625 β = 90 c = 124.063 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 IMAGE PLATE MAR scanner 300 mm plate 2007-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 69.3 98.9 49874 49874
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 95.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3EJ3 1.9 69.3 47330 47330 2544 98.93 0.20539 0.20539 0.20207 0.26861 RANDOM 16.575
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] -0.67 2.89 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.262 r_dihedral_angle_4_deg 21.624 r_dihedral_angle_3_deg 17.175 r_dihedral_angle_1_deg 6.287 r_scangle_it 3.19 r_scbond_it 2.139 r_angle_refined_deg 1.456 r_mcangle_it 1.194 r_mcbond_it 0.791 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.262 r_dihedral_angle_4_deg 21.624 r_dihedral_angle_3_deg 17.175 r_dihedral_angle_1_deg 6.287 r_scangle_it 3.19 r_scbond_it 2.139 r_angle_refined_deg 1.456 r_mcangle_it 1.194 r_mcbond_it 0.791 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5328 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 5
Software Software Software Name Purpose SERGUI data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling