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Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel 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, 0.1M sodium acetate, pH4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.7 α = 90 b = 158.7 β = 90 c = 134.6 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 2007-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.9310 ESRF ID14-3
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 2.8 93.6 0.053 24.9 4.9 2 64.602
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 2.8 2.9 89.7 0.348 5.3 5 4202
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 2.8 48.45 44771 2356 100 0.24853 0.24475 0.2184 0.32087 0.291 RANDOM 61.426
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] 0.33 0.16 0.33 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.198 r_dihedral_angle_3_deg 22.252 r_dihedral_angle_4_deg 20.708 r_dihedral_angle_1_deg 8.972 r_scangle_it 3.123 r_angle_refined_deg 2.182 r_mcangle_it 2.164 r_scbond_it 2.065 r_mcbond_it 1.292 r_nbtor_refined 0.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.198 r_dihedral_angle_3_deg 22.252 r_dihedral_angle_4_deg 20.708 r_dihedral_angle_1_deg 8.972 r_scangle_it 3.123 r_angle_refined_deg 2.182 r_mcangle_it 2.164 r_scbond_it 2.065 r_mcbond_it 1.292 r_nbtor_refined 0.352 r_nbd_refined 0.32 r_symmetry_vdw_refined 0.257 r_xyhbond_nbd_refined 0.256 r_symmetry_hbond_refined 0.196 r_chiral_restr 0.14 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11879 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 90
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction