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Structure of 3' phosphatase NExo (WT) from Neisseria bound to DNA substrate
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,
Crystal Properties Matthews coefficient Solvent content 3.66 66.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.156 α = 90 b = 59.156 β = 90 c = 292.091 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 2M 2011-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91730 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.3 48.68 99 0.07849 0.08586 0.998 13.79 6.3 153122 15625 47.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 96.9 0.582 0.63 0.239 0.95 2.2 6.8 2274
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 2.297 41.566 1.34 24060 1199 98.82 0.2001 0.1985 0.2021 0.23 0.2341
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 16.58 f_angle_d 0.616 f_chiral_restr 0.045 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2061 Nucleic Acid Atoms 317 Solvent Atoms 65 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing