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Structure and metal binding properties of ZnuA, a periplasmic zinc transporter from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PS0 PDB entry 2PS0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 7.25 mg/mL CoZnuA in buffer H (50 mM HEPES, pH 7.5, 200 mM NaCl) was mixed 1:1 with 25 % (w/v) PEG 4000, 3.5 % isopropanol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.068 α = 90 b = 78.015 β = 90 c = 85.894 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 IMAGE PLATE MAR scanner 300 mm plate mirrors 2006-07-06 M SINGLE WAVELENGTH 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B APS 5ID-B 2 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D 3 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.15 50 95.4 0.086 0.086 10.7 6.5 32326 39.4
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) 2.15 2.23 78.6 0.372 4.7 2639
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 2PS0 2.15 50 32288 1591 95.05 0.238 0.235 0.2358 0.296 0.2445 RANDOM 39.37
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] -3.62 2.91 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.022 r_dihedral_angle_4_deg 22.293 r_dihedral_angle_3_deg 15.966 r_dihedral_angle_1_deg 5.714 r_scangle_it 2.434 r_scbond_it 1.533 r_angle_refined_deg 1.267 r_mcangle_it 1.212 r_mcbond_it 0.69 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.022 r_dihedral_angle_4_deg 22.293 r_dihedral_angle_3_deg 15.966 r_dihedral_angle_1_deg 5.714 r_scangle_it 2.434 r_scbond_it 1.533 r_angle_refined_deg 1.267 r_mcangle_it 1.212 r_mcbond_it 0.69 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4072 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction