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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 2.1 41.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.82 α = 90 b = 85.6 β = 98.23 c = 55.27 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 2.3 25 99.7 0.15 10.71 4.3 18376 2
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 2.3 2.4 100 0.54 3 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 2.3 19.93 17455 919 100 0.184 0.18 0.1802 0.257 0.2561 RANDOM 18.66
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] -0.55 0.42 0.96 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.941 r_dihedral_angle_3_deg 18.045 r_dihedral_angle_4_deg 14.539 r_dihedral_angle_1_deg 6.463 r_scangle_it 2.268 r_scbond_it 1.462 r_angle_refined_deg 1.427 r_mcangle_it 0.919 r_mcbond_it 0.528 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.941 r_dihedral_angle_3_deg 18.045 r_dihedral_angle_4_deg 14.539 r_dihedral_angle_1_deg 6.463 r_scangle_it 2.268 r_scbond_it 1.462 r_angle_refined_deg 1.427 r_mcangle_it 0.919 r_mcbond_it 0.528 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.096 r_bond_refined_d 0.012 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 3618 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing