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Crystal structure of a purine nucleoside phosphorylase from Entamoeba histolytica bound to adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TL6 PDB ENTRY 3TL6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 EnhiA.01033.a.MB1 PW30572 at 22 mg/mL with 10 mM adenosine against PACT screen condition E5: 0.2 M sodium nitrate, 20% PEG3350, cryoprotectant: 25% ethylene glycol, crystal tracking ID 225630e5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.29 46.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.277 α = 90 b = 101.202 β = 90 c = 167.264 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 CCD RAYONIX MX-225 2011-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.05 50 97.9 0.104 16 6.6 90147
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 84.4 0.51 2.3 3.6 7631
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 PDB ENTRY 3TL6 2.05 50 90061 4521 97.69 0.1818 0.1798 0.1792 0.2186 0.2184 RANDOM 24.9354
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] -1.36 1.4 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.407 r_dihedral_angle_3_deg 15.444 r_dihedral_angle_4_deg 13.854 r_dihedral_angle_1_deg 6.118 r_angle_refined_deg 1.522 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10461 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 147
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxDC data collection HKL-2000 data reduction HKL-2000 data scaling