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Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate form)
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 1.5M ammonium sulfate, 100mM sodium acetate, pH4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.57 α = 90 b = 158.57 β = 90 c = 134.94 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 ADSC QUANTUM 4 mirrors 2005-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
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 2.5 20 97 0.046 18.6 3.7 64541 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 0.326 5.4 3.7 13530
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ZLQ 2.5 20 64541 1707 99.53 0.201 0.199 0.1941 0.27 0.2595 RANDOM 51.118
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] 0.51 0.26 0.51 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.225 r_dihedral_angle_4_deg 22.8 r_dihedral_angle_3_deg 20.33 r_dihedral_angle_1_deg 7.946 r_scangle_it 3.714 r_scbond_it 2.408 r_angle_refined_deg 1.963 r_mcangle_it 1.644 r_mcbond_it 0.955 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.225 r_dihedral_angle_4_deg 22.8 r_dihedral_angle_3_deg 20.33 r_dihedral_angle_1_deg 7.946 r_scangle_it 3.714 r_scbond_it 2.408 r_angle_refined_deg 1.963 r_mcangle_it 1.644 r_mcbond_it 0.955 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.294 r_nbd_refined 0.252 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.157 r_chiral_restr 0.136 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11824 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 146
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction