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Histidine 416 of the periplamsic binding protein NikA is essential for nickel uptake in Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZLQ PDB ENTRY 1ZLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 293 1.6M Ammonium sulfate, 100 mM sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.731 α = 90 b = 94.005 β = 90 c = 124.33 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 210r 2010-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.984 ESRF BM16
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 24.84 93 0.06 12.93 2.6 56622 2 27.4
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ZLQ 2.1 24.84 56622 2981 100 0.17911 0.17607 0.2369 0.2211 RANDOM 27.411
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] 0.18 -1.49 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.925 r_dihedral_angle_3_deg 16.186 r_dihedral_angle_4_deg 16.031 r_dihedral_angle_1_deg 6.408 r_scangle_it 3.946 r_scbond_it 2.501 r_angle_refined_deg 1.541 r_mcangle_it 1.518 r_mcbond_it 0.822 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.925 r_dihedral_angle_3_deg 16.186 r_dihedral_angle_4_deg 16.031 r_dihedral_angle_1_deg 6.408 r_scangle_it 3.946 r_scbond_it 2.501 r_angle_refined_deg 1.541 r_mcangle_it 1.518 r_mcbond_it 0.822 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7897 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 120
Software Software Software Name Purpose MX data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling