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Crystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 mutant Q350K
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 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.32 α = 90 b = 68.38 β = 90 c = 89.87 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 100 PIXEL DECTRIS EIGER2 X 16M 2023-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 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 1.239 50 98.5 1 21.81 12.57 95888
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 1.239 1.31 91.3 0.734 2.15 9.88
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 1.239 47.11 95888 4795 98.485 0.12 0.1189 0.1189 0.149 0.1489 20.034
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] -1.173 -0.993 2.165
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 16.433 r_dihedral_angle_6_deg 15.74 r_dihedral_angle_3_deg 12.357 r_dihedral_angle_2_deg 10.389 r_scangle_it 9.303 r_scbond_it 7 r_dihedral_angle_1_deg 6.393 r_mcangle_it 6.102 r_rigid_bond_restr 5.704 r_mcbond_it 4.539
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 16.433 r_dihedral_angle_6_deg 15.74 r_dihedral_angle_3_deg 12.357 r_dihedral_angle_2_deg 10.389 r_scangle_it 9.303 r_scbond_it 7 r_dihedral_angle_1_deg 6.393 r_mcangle_it 6.102 r_rigid_bond_restr 5.704 r_mcbond_it 4.539 r_angle_refined_deg 2.053 r_nbtor_refined 0.322 r_symmetry_nbd_refined 0.278 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.179 r_chiral_restr 0.122 r_gen_planes_refined 0.016 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2745 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing