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Re-engineered peroxygenase variant of 2-deoxy-D-ribose-5-phosphate aldolase in substrate-free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P75
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.
Crystal Properties Matthews coefficient Solvent content 2.15 42.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.173 α = 90 b = 72.752 β = 96.19 c = 70.919 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 PILATUS3 6M 2022-04-14 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 1.4 72.75 95.7 0.059 0.064 0.025 0.999 16.9 6.6 91423
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 1.4 1.42 76.5 0.796 0.875 0.354 0.746 5.5
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 MOLECULAR REPLACEMENT THROUGHOUT 1.4 50.68 86934 4462 95.48 0.13502 0.13386 0.1331 0.15708 0.157 RANDOM 17.482
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] 0.73 -1.22 -1.35 0.86
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 11.899 r_long_range_B_refined 11.897 r_dihedral_angle_3_deg 11.334 r_scangle_other 9.499 r_dihedral_angle_2_deg 8.659 r_scbond_it 6.642 r_scbond_other 6.641 r_dihedral_angle_1_deg 6.29 r_mcangle_other 5.403 r_mcangle_it 5.4
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 11.899 r_long_range_B_refined 11.897 r_dihedral_angle_3_deg 11.334 r_scangle_other 9.499 r_dihedral_angle_2_deg 8.659 r_scbond_it 6.642 r_scbond_other 6.641 r_dihedral_angle_1_deg 6.29 r_mcangle_other 5.403 r_mcangle_it 5.4 r_rigid_bond_restr 4.118 r_mcbond_it 3.839 r_mcbond_other 3.823 r_angle_refined_deg 1.678 r_angle_other_deg 0.591 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3651 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing