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Crystal structure of SLA Reductase YihU from E. Coli with NADH and product DHPS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SM7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 YihU was co-crystallized with 5mM NADH using 0.2 M Ammonium acetate, 0.1 M Bis-Tris pH 6.5, 32% PEG 3,350 as precipitant.
The crystal was then soaked with solid DHPS in the mother liquor for 2 min prior to harvesting into liquid nitrogen without any cryoprotectant.
Crystal Properties Matthews coefficient Solvent content 2.04 39.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.121 α = 90 b = 113.168 β = 90 c = 132.393 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 PILATUS 2M 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.45 86.02 100 0.067 0.071 0.025 0.999 18.2 8.1 39554
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 100 0.207 0.221 0.076 0.986 8.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6SM7 2.45 86.02 37556 1937 99.98 0.2322 0.2302 0.2327 0.2701 0.2736 RANDOM 42.027
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] -1.49 -2.62 4.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.882 r_dihedral_angle_4_deg 18.746 r_dihedral_angle_3_deg 14.606 r_dihedral_angle_1_deg 6.057 r_angle_refined_deg 1.423 r_angle_other_deg 1.321 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.882 r_dihedral_angle_4_deg 18.746 r_dihedral_angle_3_deg 14.606 r_dihedral_angle_1_deg 6.057 r_angle_refined_deg 1.423 r_angle_other_deg 1.321 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7846 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction MOLREP phasing