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Re-engineered 2-deoxy-D-ribose-5-phosphate aldolase catalysing asymmetric Michael addition reactions in substrate-free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 Protein was concentrated to 16 mg/ml in 10 mM potassium phosphate. Crystals grew from hanging-drop vapour diffusion experiments using 13% PEG 3350, 10% isopropanol and 0.1 M HEPES pH 7.5 as reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.03 39.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.634 α = 90 b = 67.497 β = 101.045 c = 73.657 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 ADSC QUANTUM 315 2021-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.229 47 96.9 0.057 0.081 0.057 0.99 6.9 2.3 128757
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.23 1.25 0.629 0.882 0.617 0.539 2.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1P1X 1.23 47 128704 6430 96.803 0.149 0.1477 0.1515 0.1714 0.1731 17.444
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] 0.342 1.091 -1.004 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.728 r_dihedral_angle_3_deg 11.039 r_dihedral_angle_4_deg 10.763 r_dihedral_angle_1_deg 6.88 r_lrange_it 2.972 r_lrange_other 2.502 r_scangle_it 1.952 r_scangle_other 1.952 r_mcangle_other 1.734 r_mcangle_it 1.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.728 r_dihedral_angle_3_deg 11.039 r_dihedral_angle_4_deg 10.763 r_dihedral_angle_1_deg 6.88 r_lrange_it 2.972 r_lrange_other 2.502 r_scangle_it 1.952 r_scangle_other 1.952 r_mcangle_other 1.734 r_mcangle_it 1.733 r_scbond_it 1.624 r_scbond_other 1.624 r_angle_other_deg 1.486 r_angle_refined_deg 1.371 r_mcbond_it 1.274 r_mcbond_other 1.269 r_rigid_bond_restr 1.014 r_symmetry_nbd_refined 0.28 r_nbd_other 0.221 r_nbd_refined 0.213 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.123 r_symmetry_xyhbond_nbd_other 0.095 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_1 0.075 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3761 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing Coot model building REFMAC refinement