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Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HVA pdb entry 2hva modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 290 MD PACT SCREEN CONDITION D9: 100MM TRIS, 20% PEG 6000, 200MM LICL, ENHIA.01206.A AT 3.8 MG/ML, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.31 46.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.14 α = 90 b = 63.14 β = 90 c = 108.37 γ = 120
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 ADSC QUANTUM 315r 2010-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 1.3 50 98.8 0.05 19.65 5.9 39679 39194 -3 18.91
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) 1.3 1.33 91.5 0.29 3.7 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2hva modified with CCP4 program CHAINSAW 1.3 48.82 39679 39193 1970 98.8 0.133 0.132 0.1437 0.155 0.1633 RANDOM 12.28
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] 0.21 0.11 0.21 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.806 r_dihedral_angle_4_deg 16.345 r_dihedral_angle_3_deg 10.558 r_dihedral_angle_1_deg 6.75 r_scangle_it 5.747 r_scbond_it 3.905 r_mcangle_it 2.902 r_mcbond_it 1.829 r_angle_refined_deg 1.772 r_angle_other_deg 0.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.806 r_dihedral_angle_4_deg 16.345 r_dihedral_angle_3_deg 10.558 r_dihedral_angle_1_deg 6.75 r_scangle_it 5.747 r_scbond_it 3.905 r_mcangle_it 2.902 r_mcbond_it 1.829 r_angle_refined_deg 1.772 r_angle_other_deg 0.964 r_rigid_bond_restr 0.903 r_mcbond_other 0.597 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1086 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 10
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling