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Structural and mechanistic insights into Helicobacter pylori NikR function
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CA9 PDB ENTRY 2CA9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.4-0.7 M AMMONIUM SULFATE, 100 MM CITRATE PH 5-5.4
Crystal Properties Matthews coefficient Solvent content 2.48 50.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.848 α = 90 b = 70.848 β = 90 c = 228.424 γ = 120
Symmetry Space Group P 61 2 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 CCD ADSC CCD 2009-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.1 47.78 99.8 0.09 8.9 8.9 20773 3 29.56
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 2.1 2.21 99.3 0.5 1.5 7.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2CA9 2.1 35.006 1.15 37356 1911 99.78 0.2004 0.1997 0.196 0.2145 0.2087 38.35
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] -2.094 -2.094 4.188
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.273 f_angle_d 0.708 f_chiral_restr 0.051 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2118 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing