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Crystal structure of NikR from Helicobacter pylori with variable Ni site coordination
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CAD PDB ENTRY 2CAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 294.5 50mM MES pH5.6, 200 mM potassium chloride, 10 mM magnesium sulfate, 5% PEG8000, vapor diffusion, sitting drop, temperature 294.5K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.479 α = 90 b = 105.056 β = 90 c = 48.185 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 105 CCD RAYONIX MX-325 2009-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 2.37 50 16660 16660
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB ENTRY 2CAD 2.37 39.34 15737 857 87.19 0.26294 0.25992 0.2616 0.31816 0.3189 RANDOM 42.44
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] -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.06 r_dihedral_angle_4_deg 18.93 r_dihedral_angle_3_deg 18.041 r_dihedral_angle_1_deg 6.493 r_scangle_it 3.92 r_scbond_it 2.32 r_angle_refined_deg 1.434 r_mcangle_it 1.4 r_mcbond_it 0.719 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.06 r_dihedral_angle_4_deg 18.93 r_dihedral_angle_3_deg 18.041 r_dihedral_angle_1_deg 6.493 r_scangle_it 3.92 r_scbond_it 2.32 r_angle_refined_deg 1.434 r_mcangle_it 1.4 r_mcbond_it 0.719 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3448 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection Web-Ice data collection