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Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dTTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IRH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 0.1 M MIB buffer (pH 5) and 25 % w/v PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.541 α = 90 b = 144.625 β = 90 c = 155.56 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD Beryllium Lenses, Diamond [111] Laue monochromator 2008-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.35 30 99.4 0.074 25.9 4.2 86389 86389 -3
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 2.35 2.43 94.9 0.43 2.1 2.6 8133
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 3IRH 2.35 29.86 81766 4304 99.45 0.18693 0.18437 0.1839 0.23461 0.2353 RANDOM 52.559
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] -1.17 -0.82 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.975 r_dihedral_angle_4_deg 16.982 r_dihedral_angle_3_deg 15.041 r_dihedral_angle_1_deg 5.285 r_scangle_it 2.015 r_scbond_it 1.216 r_angle_refined_deg 1.153 r_mcangle_it 0.762 r_mcbond_it 0.4 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.975 r_dihedral_angle_4_deg 16.982 r_dihedral_angle_3_deg 15.041 r_dihedral_angle_1_deg 5.285 r_scangle_it 2.015 r_scbond_it 1.216 r_angle_refined_deg 1.153 r_mcangle_it 0.762 r_mcbond_it 0.4 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14717 Nucleic Acid Atoms Solvent Atoms 734 Heterogen Atoms 224
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling