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Crystal Structure of a putative deoxyhypusine synthase from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P4V domains from PDB entries 6p4v and 3n89 as per Morda experimental model PDB 3N89 domains from PDB entries 6p4v and 3n89 as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 287 Microlytic MCSG1 screen, condition F3: 200mM ammonium citrate dibasic pH 5, 20% (w/V) PEG 3350: EnhiA.00933.a.A1.PW26259 at 25.43mg/ml + 4mM NAD + 4mM GC7 (Deoxyhypusine Synthase Inhibitor) : tray 314273 F3: cryo: 20% EG + compounds: puck: tds8-2
Crystal Properties Matthews coefficient Solvent content 2.88 57.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.9 α = 90 b = 85.9 β = 90 c = 424.52 γ = 120
Symmetry Space Group P 65 2 2
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 2020-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.4 50 99.9 0.068 0.072 0.999 22.39 11.678 37832 56.327
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 2.4 2.46 100 0.574 0.598 0.96 3.61 12.202
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 domains from PDB entries 6p4v and 3n89 as per Morda 2.4 42.73 1.36 37665 2010 99.91 0.1886 0.187 0.1923 0.2182 0.2222 0 64.89
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 12.482 f_angle_d 0.6459 f_chiral_restr 0.0465 f_plane_restr 0.0046 f_bond_d 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4272 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 2
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing PHENIX model building BUCCANEER model building Coot model building