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Crystal structure of E. coli dUTPase complexed with the product dUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 PEG 3350, SODIUM ACETATE, TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.257 α = 90 b = 75.257 β = 90 c = 100.532 γ = 120
Symmetry Space Group P 63 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 MARRESEARCH 2003-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8040 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.47 20 99.9 0.083 27.6 31.8 29251 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.6 100 0.73 4.86 20.09 6421
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1EUW 1.47 20 27767 27767 1484 99.98 0.15895 0.15895 0.15765 0.18384 0.1996 RANDOM 22.137
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] -0.08 -0.04 -0.08 0.11
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 10.238 r_scbond_it 6.951 r_dihedral_angle_1_deg 5.589 r_mcangle_it 3.739 r_mcbond_it 1.891 r_angle_refined_deg 1.379 r_angle_other_deg 0.737 r_symmetry_vdw_other 0.295 r_nbd_other 0.248 r_symmetry_hbond_refined 0.214
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 10.238 r_scbond_it 6.951 r_dihedral_angle_1_deg 5.589 r_mcangle_it 3.739 r_mcbond_it 1.891 r_angle_refined_deg 1.379 r_angle_other_deg 0.737 r_symmetry_vdw_other 0.295 r_nbd_other 0.248 r_symmetry_hbond_refined 0.214 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.152 r_nbtor_other 0.083 r_chiral_restr 0.076 r_bond_refined_d 0.021 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1056 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing