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Crystal structure of inactive mutant 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 2.55 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.9 α = 90 b = 74.9 β = 90 c = 99.643 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 ADSC QUANTUM 4 2003-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9392 ESRF ID14-4
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 1.7 22 98.2 0.059 8.4 20.32 18342
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 1.7 1.74 98.2 0.38 2 20.81 1268
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 1.7 20 17392 17392 949 98.2 0.18 0.15812 0.15654 0.1691 0.1872 0.2014 RANDOM 19.221
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] -0.31 -0.15 -0.31 0.46
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.45 r_scbond_it 7.396 r_dihedral_angle_1_deg 5.865 r_mcangle_it 4.712 r_angle_other_deg 2.576 r_mcbond_it 2.354 r_angle_refined_deg 1.537 r_symmetry_vdw_other 0.322 r_nbd_other 0.278 r_xyhbond_nbd_refined 0.219
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.45 r_scbond_it 7.396 r_dihedral_angle_1_deg 5.865 r_mcangle_it 4.712 r_angle_other_deg 2.576 r_mcbond_it 2.354 r_angle_refined_deg 1.537 r_symmetry_vdw_other 0.322 r_nbd_other 0.278 r_xyhbond_nbd_refined 0.219 r_symmetry_hbond_refined 0.194 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.15 r_metal_ion_refined 0.146 r_nbtor_other 0.094 r_chiral_restr 0.088 r_bond_refined_d 0.019 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1069 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing