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Crystal structures of the liganded and unliganded nickel binding protein NikA from Escherichia coli (Nickel liganded form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 PEG2000, ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.72 α = 90 b = 192.806 β = 90 c = 75.143 γ = 90
Symmetry Space Group P 21 21 2
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 2003-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0 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 1.95 20 94.6 0.041 16.7 4.2 278267 66817
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) 1.95 2.02 72.1 0.114
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.95 20 278267 66817 3588 100 0.2023 0.2023 0.19949 0.25397 0.2674 RANDOM 26.491
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] -0.31 -0.73 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.567 r_scangle_it 5.098 r_scbond_it 3.318 r_angle_refined_deg 2.09 r_mcangle_it 1.916 r_mcbond_it 1.113 r_symmetry_hbond_refined 0.371 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.236 r_chiral_restr 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.567 r_scangle_it 5.098 r_scbond_it 3.318 r_angle_refined_deg 2.09 r_mcangle_it 1.916 r_mcbond_it 1.113 r_symmetry_hbond_refined 0.371 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.236 r_chiral_restr 0.202 r_xyhbond_nbd_refined 0.169 r_bond_refined_d 0.023 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 7889 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction