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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 2.28 46.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.1 α = 90 b = 88.3 β = 97 c = 56.5 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 2 25 98.8 0.17 11.51 5.3 30031 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 2 2.1 98.4 0.64 3.47 5.4
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 2 19.88 28528 1502 100 0.188 0.186 0.1856 0.237 0.2386 RANDOM 9.75
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] 0.06 0.38 0.55 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.779 r_dihedral_angle_4_deg 17.222 r_dihedral_angle_3_deg 16.347 r_dihedral_angle_1_deg 6.994 r_scangle_it 2.649 r_scbond_it 1.737 r_angle_refined_deg 1.45 r_mcangle_it 1.078 r_mcbond_it 0.649 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.779 r_dihedral_angle_4_deg 17.222 r_dihedral_angle_3_deg 16.347 r_dihedral_angle_1_deg 6.994 r_scangle_it 2.649 r_scbond_it 1.737 r_angle_refined_deg 1.45 r_mcangle_it 1.078 r_mcbond_it 0.649 r_nbtor_refined 0.294 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.108 r_symmetry_hbond_refined 0.106 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_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 3559 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing