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Crystal structure of dUTPase complexed with substrate analogue imido-dUTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUW PDB ENTRY 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 2.54 51.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.618 α = 90 b = 74.618 β = 90 c = 99.58 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 2002-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8110 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 1.93 27.1 99.2 0.061 10.3 10 12768
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) 1.93 1.98 99.2 0.268 2.8 7.56 819
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EUW 1.93 20 12144 12144 624 99.2 0.164 0.13906 0.13701 0.1406 0.18017 0.1819 RANDOM 17.402
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] 0.11 0.05 0.11 -0.16
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.889 r_scbond_it 7.274 r_dihedral_angle_1_deg 6.006 r_mcangle_it 4.827 r_mcbond_it 2.733 r_angle_refined_deg 1.603 r_angle_other_deg 0.869 r_symmetry_vdw_other 0.355 r_nbd_other 0.259 r_symmetry_hbond_refined 0.232
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.889 r_scbond_it 7.274 r_dihedral_angle_1_deg 6.006 r_mcangle_it 4.827 r_mcbond_it 2.733 r_angle_refined_deg 1.603 r_angle_other_deg 0.869 r_symmetry_vdw_other 0.355 r_nbd_other 0.259 r_symmetry_hbond_refined 0.232 r_xyhbond_nbd_refined 0.23 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.191 r_chiral_restr 0.09 r_nbtor_other 0.085 r_bond_refined_d 0.016 r_bond_other_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1089 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing