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Structure-based enzyme engineering efforts with an inactive monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKW PDB ENTRY 1DKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 20% PEG6000, 2,5% T-BUTANOL, 0.1 M CITRIC ACID PH 5,5
Crystal Properties Matthews coefficient Solvent content 2.24 45.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.96 α = 90 b = 87.22 β = 97.5 c = 56.48 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2005-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.6 25 97.6 0.12 9.99 4.2 56766 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 96.9 0.41 3.27 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 1DKW 1.6 19.74 53925 2839 100 0.167 0.166 0.1651 0.193 0.1924 RANDOM 18.76
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] 0.42 0.51 0.18 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.583 r_dihedral_angle_4_deg 16.512 r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 5.921 r_scangle_it 3.727 r_scbond_it 2.376 r_angle_refined_deg 1.437 r_mcangle_it 1.389 r_mcbond_it 0.904 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.583 r_dihedral_angle_4_deg 16.512 r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 5.921 r_scangle_it 3.727 r_scbond_it 2.376 r_angle_refined_deg 1.437 r_mcangle_it 1.389 r_mcbond_it 0.904 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.265 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3609 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing