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Crystal structure of a deoxyuridine 5'-triphosphate nucleotidohydrolase from Burkholderia thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EU5 PDB ENTRY 1eu5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 289 ButhA.00115.a.B1.PW37235 at 35.5 mg/mL against JCSG+ C6, 40% PEG 300, 0.1 M phosphate-citrate pH 4.2, crystal tracking ID 242052c6, unique puck ID ozx5-6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.33 63.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.36 α = 90 b = 84.36 β = 90 c = 54.62 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 RAYONIX MX-300 2012-06-19 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) 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 1.5 50 100 0.047 34.27 15.3 35554 35545 -3
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 1.5 1.54 100 0.454 5.02
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 1eu5 1.5 43.78 33748 1778 99.97 0.11805 0.11718 0.141 0.13471 0.1515 RANDOM 23.149
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] 0.06 0.06 0.06 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.693 r_sphericity_free 30.54 r_dihedral_angle_4_deg 24.038 r_dihedral_angle_3_deg 12.029 r_sphericity_bonded 8.134 r_dihedral_angle_1_deg 5.725 r_rigid_bond_restr 2.262 r_scbond_it 2.173 r_mcangle_it 2.019 r_mcbond_it 1.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.693 r_sphericity_free 30.54 r_dihedral_angle_4_deg 24.038 r_dihedral_angle_3_deg 12.029 r_sphericity_bonded 8.134 r_dihedral_angle_1_deg 5.725 r_rigid_bond_restr 2.262 r_scbond_it 2.173 r_mcangle_it 2.019 r_mcbond_it 1.556 r_mcbond_other 1.457 r_angle_refined_deg 1.387 r_angle_other_deg 0.736 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1006 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 13
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction