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NADPH complex of Imine Reductase from Pochonia chlamydosporia 170
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 PEG 3350, magnesium chloride, Tris-Hcl 8.5
Crystal Properties Matthews coefficient Solvent content 2.17 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.802 α = 90 b = 114.091 β = 99.34 c = 62.87 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 Bruker PHOTON III 2023-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.09 33.08 99.1 0.0538 17.53 5.29 30773
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 2.09 2.13 88.1 0.1537 4.33 2.67
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 2.1 33.08 28926 1540 99.44 0.18502 0.18128 0.189 0.25489 0.2589 RANDOM 30.787
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] 4.54 0.65 -1.85 -2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.847 r_dihedral_angle_4_deg 16.525 r_dihedral_angle_3_deg 16.296 r_dihedral_angle_1_deg 6.315 r_long_range_B_refined 5.46 r_long_range_B_other 5.455 r_scangle_other 3.953 r_mcangle_it 3.116 r_mcangle_other 3.115 r_scbond_it 2.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.847 r_dihedral_angle_4_deg 16.525 r_dihedral_angle_3_deg 16.296 r_dihedral_angle_1_deg 6.315 r_long_range_B_refined 5.46 r_long_range_B_other 5.455 r_scangle_other 3.953 r_mcangle_it 3.116 r_mcangle_other 3.115 r_scbond_it 2.554 r_scbond_other 2.554 r_mcbond_it 2.088 r_mcbond_other 2.088 r_angle_refined_deg 1.579 r_angle_other_deg 1.297 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 4221 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SAINT data reduction PHASER phasing