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Imine Reductase IR91 from Kribbella flavida with NADP+ and 5-methoxy-(S)-2-(N-methylamino)tetralin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JIT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M btp buffer pH 5.5; 25% (w/v) PEG 3350; 0.2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.46 50.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.8 α = 90 b = 109.51 β = 93.93 c = 53.75 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 EIGER2 XE 16M 2022-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97627 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 1.91 109.51 100 0.16 0.06 1 7.6 6.9 46333
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 1.91 1.95 1.02 0.42 0.78 1
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 1.91 54.76 44044 2254 99.99 0.1898 0.1876 0.1986 0.23533 0.2456 RANDOM 26.265
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] -1.7 -1.6 -2.55 4.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.41 r_dihedral_angle_2_deg 9.441 r_long_range_B_refined 6.215 r_long_range_B_other 6.105 r_dihedral_angle_1_deg 5.954 r_scangle_other 4.634 r_mcangle_it 3.686 r_mcangle_other 3.685 r_scbond_it 3.162 r_scbond_other 3.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.41 r_dihedral_angle_2_deg 9.441 r_long_range_B_refined 6.215 r_long_range_B_other 6.105 r_dihedral_angle_1_deg 5.954 r_scangle_other 4.634 r_mcangle_it 3.686 r_mcangle_other 3.685 r_scbond_it 3.162 r_scbond_other 3.118 r_mcbond_it 2.588 r_mcbond_other 2.588 r_angle_refined_deg 1.555 r_angle_other_deg 0.482 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 4185 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing