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Structure of Reductive Aminase from Aspergillus terreus in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 31% (w/v) PEG 3350; 0.2 M MgCl2, 0.1 M Tris HCl pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.977 α = 90 b = 85.552 β = 90 c = 355.423 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M-F 2015-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.2 177.71 100 0.1 0.05 1 13.2 8.1 118787
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 2.2 2.24 100 0.73 0.4 0.83 2.7 8.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5G6R 2.2 177.71 112724 5951 99.96 0.20035 0.19848 0.23581 0.2242 RANDOM 41.387
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] 0.89 0.8 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.597 r_dihedral_angle_4_deg 22.559 r_dihedral_angle_3_deg 15.144 r_long_range_B_refined 8.254 r_long_range_B_other 8.243 r_scangle_other 6.428 r_dihedral_angle_1_deg 6.222 r_mcangle_it 5.448 r_mcangle_other 5.448 r_scbond_it 4.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.597 r_dihedral_angle_4_deg 22.559 r_dihedral_angle_3_deg 15.144 r_long_range_B_refined 8.254 r_long_range_B_other 8.243 r_scangle_other 6.428 r_dihedral_angle_1_deg 6.222 r_mcangle_it 5.448 r_mcangle_other 5.448 r_scbond_it 4.451 r_scbond_other 4.451 r_mcbond_it 3.845 r_mcbond_other 3.844 r_angle_refined_deg 1.748 r_angle_other_deg 1.067 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 15643 Nucleic Acid Atoms Solvent Atoms 823 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data scaling MOLREP phasing