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Copper-bound C-terminal Domain of NikR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q5Y The tetramer of nickel-bound c-terminal domain of NikR, 1Q5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.2M Na Tartrate, 20% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.89 34.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.949 α = 90 b = 78.442 β = 90 c = 81.46 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 100 CCD ADSC QUANTUM 315 2004-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 8-BM 0.9791 APS 8-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 50 97.9 0.059 0.057 16.9 8.1 47685 46684
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.55 85.2 0.263 0.254 5.3 6.1 4006
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT The tetramer of nickel-bound c-terminal domain of NikR, 1Q5Y 1.5 15.17 46684 46629 2360 97.94 0.198 0.198 0.196 0.2001 0.227 0.2327 RANDOM 16.047
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] 0.04 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.752 r_dihedral_angle_4_deg 17.066 r_dihedral_angle_3_deg 14.148 r_sphericity_free 6.882 r_dihedral_angle_1_deg 5.878 r_scangle_it 3.8 r_sphericity_bonded 3.062 r_scbond_it 2.808 r_rigid_bond_restr 2.663 r_mcangle_it 2.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.752 r_dihedral_angle_4_deg 17.066 r_dihedral_angle_3_deg 14.148 r_sphericity_free 6.882 r_dihedral_angle_1_deg 5.878 r_scangle_it 3.8 r_sphericity_bonded 3.062 r_scbond_it 2.808 r_rigid_bond_restr 2.663 r_mcangle_it 2.105 r_mcbond_it 1.403 r_angle_refined_deg 1.346 r_angle_other_deg 0.877 r_mcbond_other 0.527 r_symmetry_hbond_refined 0.219 r_nbd_refined 0.209 r_nbd_other 0.187 r_symmetry_vdw_other 0.183 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.159 r_nbtor_other 0.086 r_chiral_restr 0.085 r_metal_ion_refined 0.04 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2618 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XFIT data reduction