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Crystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 mutant T354K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 25 mM sodium phosphate pH 7.2, 75 mM NaCl, 25 mM Tris-HCl pH 8.5, 0.1 M NH4Cl, 5 mM CaCl2, 15% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.12 42.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.5 α = 90 b = 68.08 β = 93.7 c = 91.71 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 DECTRIS EIGER2 X 16M 2024-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03321 PETRA III, DESY P11
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 1.44 48.8 98.8 0.998 9.63 6.84 120777
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.53 98.3 0.526 1.2 6.54
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.444 48.799 120775 6039 98.764 0.144 0.1418 0.1463 0.1868 0.1775 17.436
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] -0.397 0.427 -0.74 1.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.4 r_lrange_it 13.41 r_dihedral_angle_3_deg 12.448 r_dihedral_angle_2_deg 9.983 r_scangle_it 7.502 r_dihedral_angle_1_deg 6.293 r_mcangle_it 5.413 r_scbond_it 5.344 r_rigid_bond_restr 4.546 r_mcbond_it 3.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.4 r_lrange_it 13.41 r_dihedral_angle_3_deg 12.448 r_dihedral_angle_2_deg 9.983 r_scangle_it 7.502 r_dihedral_angle_1_deg 6.293 r_mcangle_it 5.413 r_scbond_it 5.344 r_rigid_bond_restr 4.546 r_mcbond_it 3.792 r_angle_refined_deg 1.828 r_nbtor_refined 0.316 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.167 r_chiral_restr 0.129 r_gen_planes_refined 0.012 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5478 Nucleic Acid Atoms Solvent Atoms 900 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing