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Cobalt bound structure of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Crystallization was carried out in hanging-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 0.7 mM Cko and 10 mM CoCl2 and reservoir solution containing 20% PEG 3350 and 0.2 M Na2HPO4 , pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.89 34.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.74 α = 90 b = 58.4 β = 102.55 c = 33.05 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 130 PIXEL PSI PILATUS 6M 2011-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.282 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.52 28.24 98.8 15894 15703 -99 -99
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) 1 1.52 1.6 98.8 0.038 17.7 3 15703
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 3PH4 1.52 24.565 1.35 15679 1595 98.73 0.1597 0.1564 0.1543 0.1886 0.1865 RANDOM
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] 0.4907 2.3892 -1.837 0.4094
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.682 f_angle_d 1.297 f_chiral_restr 0.091 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 967 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 13
Software Software Software Name Purpose CBASS data collection PHENIX model building PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing