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Re-engineered peroxygenase variant of 2-deoxy-D-ribose-5-phosphate aldolase, Schiff-base complex with 4-nitro-cinnamaldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Crystal structure of the apo enzyme was used as initial model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 Protein was concentrated to 8 mg/mL in 20 mM potassium phosphate, pH 7. Crystallization conditions: 0-4% 2-propanol, 22-24% PEG 3350 in 0.1 M HEPES, pH 7.5. The Schiff-base complex was obtained by brief soaking (about 30 seconds) in saturated ligand solution prepared with crystallization solution plus 25% glycerol
Crystal Properties Matthews coefficient Solvent content 2.13 42.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.095 α = 90 b = 72.531 β = 96.27 c = 70.688 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 PIXEL DECTRIS PILATUS 6M 2022-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 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 1.52 47.81 95.5 0.09 0.115 0.072 0.988 7 2.3 70796
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 1.52 1.55 93.6 1.155 1.471 0.9 0.312 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 1.52 41.73 67356 3406 95.28 0.18777 0.18633 0.1993 0.21755 0.2308 RANDOM 20.473
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] -0.35 0.04 0.69 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.214 r_dihedral_angle_2_deg 9.532 r_dihedral_angle_1_deg 6.542 r_long_range_B_refined 5.27 r_long_range_B_other 5.212 r_scangle_other 4.068 r_scbond_it 2.605 r_scbond_other 2.605 r_mcangle_it 1.991 r_mcangle_other 1.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.214 r_dihedral_angle_2_deg 9.532 r_dihedral_angle_1_deg 6.542 r_long_range_B_refined 5.27 r_long_range_B_other 5.212 r_scangle_other 4.068 r_scbond_it 2.605 r_scbond_other 2.605 r_mcangle_it 1.991 r_mcangle_other 1.991 r_angle_refined_deg 1.782 r_mcbond_it 1.362 r_mcbond_other 1.331 r_angle_other_deg 0.597 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3642 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing