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dCTP deaminase from Escherichia coli- E138A mutant enzyme in complex with dCTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGH PDB ENTRY 1OGH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG 400, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.272 α = 90 b = 97.882 β = 109.23 c = 95.116 γ = 90
Symmetry Space Group P 1 21 1
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 Vertically focusing cylindrical mirror. 2003-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.969 MAX II I711
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 2.53 30 98.5 0.052 25.6 3.7 37005 37005
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) 2.53 2.59 78.2 0.092 12.5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION combination of SAD and MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OGH 2.53 30 36399 34581 1818 99.44 0.18689 0.18479 0.22541 0.2534 RANDOM 19.611
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] 0.85 -0.08 0.3 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.608 r_scangle_it 3.387 r_scbond_it 2.077 r_angle_refined_deg 1.66 r_mcangle_it 1.289 r_angle_other_deg 0.962 r_mcbond_it 0.679 r_symmetry_vdw_other 0.261 r_nbd_other 0.251 r_nbd_refined 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.608 r_scangle_it 3.387 r_scbond_it 2.077 r_angle_refined_deg 1.66 r_mcangle_it 1.289 r_angle_other_deg 0.962 r_mcbond_it 0.679 r_symmetry_vdw_other 0.261 r_nbd_other 0.251 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.178 r_symmetry_vdw_refined 0.16 r_chiral_restr 0.095 r_nbtor_other 0.086 r_metal_ion_refined 0.075 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8952 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing