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Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.1 M HEPES sodium salt pH 7.5, 2 %(v/v) PEG 400, 2.0 M Ammonium sulfate, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.99 58.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.379 α = 90 b = 79.4 β = 122.28 c = 122.423 γ = 90
Symmetry Space Group C 1 2 1
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 QUANTUM 315 2010-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.000 SSRL BL7-1
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 3.08 103.5 21352
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.08 103.5 19187 2165 95.53 0.26195 0.25726 0.30361 0.282 RANDOM 48.803
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] -5.88 -0.44 4.74 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.43 r_dihedral_angle_4_deg 21.375 r_dihedral_angle_3_deg 19.697 r_dihedral_angle_1_deg 7.311 r_scangle_it 2.73 r_mcangle_it 1.842 r_scbond_it 1.834 r_angle_refined_deg 1.669 r_angle_other_deg 1.269 r_mcbond_it 0.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.43 r_dihedral_angle_4_deg 21.375 r_dihedral_angle_3_deg 19.697 r_dihedral_angle_1_deg 7.311 r_scangle_it 2.73 r_mcangle_it 1.842 r_scbond_it 1.834 r_angle_refined_deg 1.669 r_angle_other_deg 1.269 r_mcbond_it 0.991 r_chiral_restr 0.167 r_mcbond_other 0.123 r_bond_refined_d 0.017 r_bond_other_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6104 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction