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Reductive aminase RA29-WT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289.2 calcium acetate trihydrate,PEG3350
Crystal Properties Matthews coefficient Solvent content 2.17 43.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.521 α = 90 b = 95.904 β = 96.88 c = 67.395 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 150 PIXEL Bruker PHOTON II multilyer 2023-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54178
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 2.03 42.25 99.1 0.114 13.4 5.6 34365
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 2.03 2.08 0.453
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 2.03 42.25 32600 1735 99.07 0.2014 0.19945 0.2071 0.23751 0.2389 RANDOM 20.518
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] 1.56 0.77 -1.69 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.047 r_dihedral_angle_4_deg 19.368 r_dihedral_angle_3_deg 12.741 r_dihedral_angle_1_deg 5.507 r_long_range_B_refined 3.428 r_long_range_B_other 3.334 r_scangle_other 2.222 r_mcangle_it 1.68 r_mcangle_other 1.68 r_angle_refined_deg 1.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.047 r_dihedral_angle_4_deg 19.368 r_dihedral_angle_3_deg 12.741 r_dihedral_angle_1_deg 5.507 r_long_range_B_refined 3.428 r_long_range_B_other 3.334 r_scangle_other 2.222 r_mcangle_it 1.68 r_mcangle_other 1.68 r_angle_refined_deg 1.407 r_scbond_it 1.384 r_scbond_other 1.384 r_mcbond_it 1.014 r_mcbond_other 1.012 r_angle_other_deg 0.801 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4198 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 104
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction PROTEUM PLUS data reduction PROTEUM PLUS data scaling