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Crystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 mutant D352K
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 41.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.4 α = 90 b = 68.16 β = 94.07 c = 91.63 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 1.43 50 98.3 0.997 10.36 5.12 122540
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 1.43 1.52 96.8 0.565 1.37 4.98
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.433 48.849 122540 6127 98.263 0.153 0.1508 0.1949 0.1951 17.229
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] -0.03 0.505 -1.042 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.583 r_dihedral_angle_3_deg 12.429 r_lrange_it 12.186 r_dihedral_angle_2_deg 10.785 r_scangle_it 7.468 r_dihedral_angle_1_deg 6.19 r_mcangle_it 5.489 r_scbond_it 5.333 r_rigid_bond_restr 4.333 r_mcbond_it 3.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.583 r_dihedral_angle_3_deg 12.429 r_lrange_it 12.186 r_dihedral_angle_2_deg 10.785 r_scangle_it 7.468 r_dihedral_angle_1_deg 6.19 r_mcangle_it 5.489 r_scbond_it 5.333 r_rigid_bond_restr 4.333 r_mcbond_it 3.813 r_angle_refined_deg 1.743 r_nbtor_refined 0.315 r_symmetry_nbd_refined 0.228 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.15 r_chiral_restr 0.113 r_gen_planes_refined 0.013 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5492 Nucleic Acid Atoms Solvent Atoms 882 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing