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Crystal Structure of S-adenosyl-L-homocysteine hydrolase from Acanthamoeba castellanii with bound NAD and Adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 AccaA.00032.a.B1.PW38645 at 20.81 mg/ml, incubated with 2 mM NAD, SAH, mixed 1:1 with 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M MOPS/HEPES-Na, pH=7.5, 0.02 M of sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, 0.2 M sodium oxamate. Tray: 311079g8, puck: ved0-8
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.03 α = 90 b = 112.73 β = 114.725 c = 105.92 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 CCD RAYONIX MX-300 Beryllium Lenses 2019-08-01 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 1.4 50 99.7 0.044 0.05 0.999 16.63 4.142 400199 22.399
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 1.4 1.44 99.5 0.584 0.67 0.801 2.2 4.125
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5v96 1.4 50 1.34 400168 2000 99.75 0.1301 0.1299 0.1304 0.1611 0.1615 22.17
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 16.2128 f_angle_d 0.8622 f_chiral_restr 0.0824 f_bond_d 0.0051 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14732 Nucleic Acid Atoms Solvent Atoms 2329 Heterogen Atoms 309
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction ARP/wARP model building