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Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145A from Methanocaldococcus jannaschii in complex with alpha,beta-imido dUTP and magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HXB PDB ENTRY 2HXB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.2 298 20 % PEG3350, 0.2M di-potassium hydrogen phosphate, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.44 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.513 α = 90 b = 171.513 β = 90 c = 171.513 γ = 90
Symmetry Space Group I 4 3 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 2005-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.072300 ESRF ID23-1
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 2.3 25 100 0.089 14.4 4.36 18566 18566
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 2.3 2.42 98.9 0.432 3 3.9 2746
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2HXB 2.3 24.75 18560 17636 924 100 0.18 0.178 0.1874 0.221 0.2298 RANDOM 27.131
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_dihedral_angle_4_deg 20.96 r_dihedral_angle_3_deg 17.328 r_dihedral_angle_1_deg 7.496 r_scangle_it 3.739 r_scbond_it 2.643 r_angle_refined_deg 1.844 r_mcangle_it 1.591 r_mcbond_it 1.376 r_angle_other_deg 0.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_dihedral_angle_4_deg 20.96 r_dihedral_angle_3_deg 17.328 r_dihedral_angle_1_deg 7.496 r_scangle_it 3.739 r_scbond_it 2.643 r_angle_refined_deg 1.844 r_mcangle_it 1.591 r_mcbond_it 1.376 r_angle_other_deg 0.942 r_symmetry_vdw_other 0.302 r_symmetry_vdw_refined 0.248 r_mcbond_other 0.197 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.187 r_nbd_other 0.182 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.173 r_chiral_restr 0.101 r_nbtor_other 0.088 r_bond_refined_d 0.022 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1606 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOSFLM data reduction SCALA data scaling