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Crystal Structure of Fumarate hydratase class II from Elizabethkingia anophelis NUHP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TV2 pdb 3tv2 chain A in three domains as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 Rigaku Reagents JCSG TOP96 screen, condition #61/F1: 20% PEG 3350, 200mM Ammonium formate: ElanA.00047.b.B1.PS38159 at 25mg/ml: tray 318833 F1: cryo: 20% EG: puck NDH4-7.
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.76 α = 116.151 b = 92.65 β = 107.668 c = 98.43 γ = 90.032
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 Beryllium Lenses 2020-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.25 50 94.2 0.038 0.044 0.999 20.17 3.876 465944 14.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.28 90.6 0.266 0.318 0.936 4.32 3.33
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE pdb 3tv2 chain A in three domains as per Morda 1.25 35.94 1.99 465896 10052 94.39 0.1245 0.124 0.1239 0.1472 0.1469 0 16.35
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.6364 f_angle_d 0.9183 f_chiral_restr 0.0807 f_plane_restr 0.0081 f_bond_d 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14084 Nucleic Acid Atoms Solvent Atoms 2529 Heterogen Atoms 8
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing ARP/wARP model building PHENIX model building Coot model building