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Crystal structure of a E138A Escherichia coli dCTP deaminase mutant enzyme in complex with dTTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XS1 PDB ENTRY 1XS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.8 VAPOUR DIFFUSION, 34% PEG400, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH6.8, 5MM DCTP
Crystal Properties Matthews coefficient Solvent content 2.5 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.594 α = 90 b = 61.594 β = 90 c = 344.766 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 2003-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
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 2.6 50 92.7 0.14 21.9 12.2 12085
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 2.6 2.74 70 0.52 2.6 5.5
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 1XS1 2.6 30 11438 582 92.6 0.25 0.247 0.2615 0.302 0.3217 RANDOM 29.15
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] 2.26 1.13 2.26 -3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.017 r_dihedral_angle_4_deg 23.781 r_dihedral_angle_3_deg 18.017 r_dihedral_angle_1_deg 7.543 r_scangle_it 2.524 r_angle_refined_deg 1.716 r_scbond_it 1.666 r_mcangle_it 1.22 r_mcbond_it 1.082 r_angle_other_deg 1.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.017 r_dihedral_angle_4_deg 23.781 r_dihedral_angle_3_deg 18.017 r_dihedral_angle_1_deg 7.543 r_scangle_it 2.524 r_angle_refined_deg 1.716 r_scbond_it 1.666 r_mcangle_it 1.22 r_mcbond_it 1.082 r_angle_other_deg 1.027 r_chiral_restr 0.242 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.218 r_symmetry_vdw_other 0.209 r_symmetry_hbond_refined 0.199 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.149 r_nbtor_other 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2641 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing