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Holo-Ni(II) HpNikR is a symmetric tetramer containing four canonic square-planar Ni(II) ions at physiological pH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.3 20% PEG 3350 AND 0.2 M K/NA-TARTRATE, pH 7.3
Crystal Properties Matthews coefficient Solvent content 4.05 69.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.97 α = 90 b = 72.97 β = 90 c = 116.73 γ = 90
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 MARRESEARCH 2010-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 EMBL/DESY, HAMBURG X12
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 2.39 19.94 99.8 0.07 26.8 14 24202 3.5 52.396
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 2.39 2.52 100 0.64 3.5 8.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT NONE 2.39 72.98 21766 1177 94.78 0.2317 0.22917 0.27892 0.2216 RANDOM 43.377
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] -0.26 -0.26 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.883 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 19.572 r_dihedral_angle_1_deg 7.667 r_scangle_it 6.428 r_scbond_it 3.966 r_mcangle_it 2.803 r_angle_refined_deg 2.216 r_mcbond_it 1.496 r_chiral_restr 0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.883 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 19.572 r_dihedral_angle_1_deg 7.667 r_scangle_it 6.428 r_scbond_it 3.966 r_mcangle_it 2.803 r_angle_refined_deg 2.216 r_mcbond_it 1.496 r_chiral_restr 0.163 r_bond_refined_d 0.026 r_gen_planes_refined 0.009 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2686 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling HKL2Map phasing