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Structure and Activities of Archaeal Members of the LigD 3' Phosphoesterase DNA Repair Enzyme Superfamily
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N9B PDB ENTRY 3N9B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 vapor-diffusion, sitting-drop setups with 1:1 mixtures of protein solution containing 0.5 mM Mba and 2mM MnCl2 and reservoir solution containing PEG 4000 (32%), 0.18 M MgCl2, 2.5% 1,4-dioxane, 0.1 M Tris-HCl pH 7.5, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 1.99 38.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.368 α = 90 b = 60.166 β = 90 c = 76.471 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 130 CCD ADSC QUANTUM 315 2010-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 2.1 38.236 97.5 0.122 11.12 4.9 8827 8606 -3 20.6
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) 2.1 2.18 97.2 0.465 2.74 3.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 3N9B 2.1 38.236 1 8458 847 97.52 0.2086 0.2029 0.2012 0.2572 0.2546 Random 23.1
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] -3.9711 -5.1005 9.0717
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.322 f_angle_d 0.95 f_chiral_restr 0.066 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1004 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 7
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling