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Structure of 3' phosphatase NExo (D146N) from Neisseria bound to product DNA hairpin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 277 100 mM imidazole pH = 6.6,
55 mM (NH4)2SO4,
10% (w/v) PEG 8000,
16 - 19 % (v/v) MPD,
MnCl2
Crystal Properties Matthews coefficient Solvent content 3.74 67.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.929 α = 90 b = 58.929 β = 90 c = 292.591 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 6M 2013-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96860 Diamond I24
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 2.02 54.53 100 0.241 2.34 2 35624
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 2.02 2.08 0.5079
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2JC4 2.151 40.075 1.37 29065 1223 99.05 0.2011 0.2001 0.1999 0.2241 0.2213
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.264 f_angle_d 0.956 f_chiral_restr 0.066 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2061 Nucleic Acid Atoms 247 Solvent Atoms 173 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing