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Crystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 mutant Q204K
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 2.1 41.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.36 α = 90 b = 68.56 β = 90 c = 90.04 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 99.5 0.999 15.05 9.31 97454
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 1.24 1.31 97 0.522 1.32 6.66
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 47.159 97454 4873 99.465 0.131 0.1289 0.1288 0.1633 0.1632 18.414
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] -0.894 -0.898 1.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.584 r_lrange_it 13.104 r_dihedral_angle_3_deg 12.232 r_dihedral_angle_2_deg 11.024 r_scangle_it 8.395 r_dihedral_angle_1_deg 6.339 r_scbond_it 6.155 r_mcangle_it 5.572 r_rigid_bond_restr 4.927 r_mcbond_it 4.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.584 r_lrange_it 13.104 r_dihedral_angle_3_deg 12.232 r_dihedral_angle_2_deg 11.024 r_scangle_it 8.395 r_dihedral_angle_1_deg 6.339 r_scbond_it 6.155 r_mcangle_it 5.572 r_rigid_bond_restr 4.927 r_mcbond_it 4.011 r_angle_refined_deg 1.922 r_nbtor_refined 0.318 r_symmetry_nbd_refined 0.247 r_symmetry_xyhbond_nbd_refined 0.212 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.12 r_gen_planes_refined 0.015 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2745 Nucleic Acid Atoms Solvent Atoms 467 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing