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Crystal structures of the liganded and unliganded nickel binding protein NikA from Escherichia coli (Nickel unliganded form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.869 α = 90 b = 126.869 β = 90 c = 60.523 γ = 120
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 MAR CCD 165 mm mirrors 2003-01-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.9793, 0.9797, 0.9824 SPring-8 BL44B2
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 1.85 20 91.1 0.045 17.5 2.5 206476 81622
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) 1.85 1.92 78.6 0.384
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.85 19.96 206476 77485 4104 100 0.20048 0.20048 0.19803 0.1995 0.24729 0.245 RANDOM 33.078
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] 0.91 0.45 0.91 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.996 r_scangle_it 4.614 r_scbond_it 3.022 r_angle_refined_deg 1.95 r_mcangle_it 1.884 r_mcbond_it 1.125 r_symmetry_hbond_refined 0.366 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.194 r_chiral_restr 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.996 r_scangle_it 4.614 r_scbond_it 3.022 r_angle_refined_deg 1.95 r_mcangle_it 1.884 r_mcbond_it 1.125 r_symmetry_hbond_refined 0.366 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.194 r_chiral_restr 0.191 r_xyhbond_nbd_refined 0.177 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7882 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling SOLVE phasing REFMAC refinement HKL-2000 data reduction