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Reductive Aminase from Aspergillus terreus in complex with NADPH4, cyclohexanone and allyl amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EOD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 100 mM Tris-HCl pH 8.5, 34% PEG 3350, 0.2M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.206 α = 90 b = 162.83 β = 108.67 c = 49.681 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 120 PIXEL DECTRIS PILATUS3 S 6M 2017-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.79 47.07 95.8 0.06 0.05 0.99 10.5 3.8 52888
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.83 99.8 0.33 0.27 0.94 2.5 4.1
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 6EOD 1.79 40.74 47890 2474 91.06 0.24858 0.24734 0.2554 0.27175 0.2752 RANDOM 28.496
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] -0.19 -1.82 -2.74 3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.838 r_dihedral_angle_4_deg 22.483 r_dihedral_angle_3_deg 13.38 r_dihedral_angle_1_deg 6.346 r_long_range_B_refined 5.516 r_long_range_B_other 5.491 r_scangle_other 3.924 r_mcangle_it 3.004 r_mcangle_other 3.004 r_scbond_it 2.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.838 r_dihedral_angle_4_deg 22.483 r_dihedral_angle_3_deg 13.38 r_dihedral_angle_1_deg 6.346 r_long_range_B_refined 5.516 r_long_range_B_other 5.491 r_scangle_other 3.924 r_mcangle_it 3.004 r_mcangle_other 3.004 r_scbond_it 2.569 r_scbond_other 2.569 r_mcbond_it 1.995 r_mcbond_other 1.994 r_angle_refined_deg 1.316 r_angle_other_deg 0.946 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 4057 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing