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Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O6I PDB ID 2O6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 295 0.2 M Sodium bromide, 0.1 M Bis-tris propane pH 7.5, 20 % w/v Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.14 42.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.253 α = 90 b = 188.66 β = 90 c = 67.822 γ = 90
Symmetry Space Group P 21 21 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 BERYLLIUM LENSES/DIAMOND LAUE MONO 2008-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 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 2.4 30 99.1 0.08 21 3.9 75951 -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 2.4 2.49 95.3 0.55 2.4 1.9
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 ID 2O6I 2.4 30 71324 3783 99.2 0.188 0.185 0.1872 0.244 0.1844 RANDOM 40.67
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] -5.12 2.09 3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.703 r_dihedral_angle_4_deg 16.627 r_dihedral_angle_3_deg 15.873 r_dihedral_angle_1_deg 5.493 r_scangle_it 3.06 r_scbond_it 1.907 r_mcangle_it 1.211 r_angle_refined_deg 1.21 r_mcbond_it 0.693 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.703 r_dihedral_angle_4_deg 16.627 r_dihedral_angle_3_deg 15.873 r_dihedral_angle_1_deg 5.493 r_scangle_it 3.06 r_scbond_it 1.907 r_mcangle_it 1.211 r_angle_refined_deg 1.21 r_mcbond_it 0.693 r_nbtor_refined 0.304 r_metal_ion_refined 0.245 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.201 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14635 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 188
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling