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Crystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 (engineered Loop Swap from Achromobacter sp. JA81)
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, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.22 α = 90 b = 67.78 β = 93.52 c = 91.52 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 EIGER X 16M 2022-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99999 SLS X06SA
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 1.27 48.53 97.52 0.999 15.95 6.75 178747
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 1.27 1.34 90.9 0.649 1.82 5.6
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 1.27 48.528 173245 8663 97.739 0.132 0.1302 0.1302 0.1614 0.1615 16.64
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] -0.513 -0.444 0.349 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.076 r_lrange_it 13.295 r_dihedral_angle_3_deg 12.022 r_dihedral_angle_2_deg 10.943 r_scangle_it 7.734 r_dihedral_angle_1_deg 6.141 r_scbond_it 5.807 r_mcangle_it 5.33 r_rigid_bond_restr 4.998 r_mcbond_it 3.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.076 r_lrange_it 13.295 r_dihedral_angle_3_deg 12.022 r_dihedral_angle_2_deg 10.943 r_scangle_it 7.734 r_dihedral_angle_1_deg 6.141 r_scbond_it 5.807 r_mcangle_it 5.33 r_rigid_bond_restr 4.998 r_mcbond_it 3.896 r_angle_refined_deg 1.912 r_nbtor_refined 0.316 r_symmetry_nbd_refined 0.258 r_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.194 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.12 r_gen_planes_refined 0.015 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5490 Nucleic Acid Atoms Solvent Atoms 1151 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing