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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 Other ZnZnuA in space group P212121
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 30 % (w/v) PEG 4000, 5 % isopropanol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.377 α = 90 b = 78.073 β = 91.37 c = 86.366 γ = 90
Symmetry Space Group C 1 2 1
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 345 mm plate mirrors 2006-04-07 M SINGLE WAVELENGTH 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1 2 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID 3 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 1.7 28.8 97.2 0.053 3.6 64618 32.5
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) 1.7 1.76 85.5 0.323 3.1 5643
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 ZnZnuA in space group P212121 1.7 28.8 64618 64597 3254 97 0.213 0.211 0.2102 0.25 0.2495 RANDOM 32.48
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] 0.04 -0.18 1.4 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.948 r_dihedral_angle_4_deg 16.565 r_dihedral_angle_3_deg 13.809 r_dihedral_angle_1_deg 5.665 r_scangle_it 2.856 r_scbond_it 1.773 r_mcangle_it 1.263 r_angle_refined_deg 1.22 r_mcbond_it 0.756 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.948 r_dihedral_angle_4_deg 16.565 r_dihedral_angle_3_deg 13.809 r_dihedral_angle_1_deg 5.665 r_scangle_it 2.856 r_scbond_it 1.773 r_mcangle_it 1.263 r_angle_refined_deg 1.22 r_mcbond_it 0.756 r_nbtor_refined 0.301 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.081 r_metal_ion_refined 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4160 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 3
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction PHASER phasing