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Crystal structure of DnaD domain protein from Enterococcus faecalis. Structural genomics target APC85179
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.2M Magnesium chloride, 25% PEG3350, pH 5.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.02 38.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.795 α = 90 b = 48.795 β = 90 c = 32.795 γ = 90
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 ADSC QUANTUM 315 2006-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97835 APS 19-ID
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 1.5 50 97.3 0.071 32.68 8.8 22919 22919
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 1.5 1.55 88.5 0.422 2.13 5 1078
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.5 34.5 11725 11725 596 98.44 0.18175 0.18175 0.17957 0.1865 0.22702 0.2212 RANDOM 17.772
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.427 r_dihedral_angle_4_deg 17.771 r_dihedral_angle_3_deg 16.634 r_dihedral_angle_1_deg 4.773 r_scangle_it 3.187 r_scbond_it 2.271 r_angle_other_deg 1.525 r_mcangle_it 1.221 r_mcbond_it 1.072 r_angle_refined_deg 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.427 r_dihedral_angle_4_deg 17.771 r_dihedral_angle_3_deg 16.634 r_dihedral_angle_1_deg 4.773 r_scangle_it 3.187 r_scbond_it 2.271 r_angle_other_deg 1.525 r_mcangle_it 1.221 r_mcbond_it 1.072 r_angle_refined_deg 1.02 r_symmetry_hbond_refined 0.303 r_symmetry_vdw_other 0.299 r_xyhbond_nbd_refined 0.221 r_nbd_refined 0.2 r_mcbond_other 0.193 r_nbtor_refined 0.192 r_nbd_other 0.178 r_symmetry_vdw_refined 0.162 r_nbtor_other 0.087 r_chiral_restr 0.075 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 625 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building