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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 4.6 293 5 mg/mL protein in 20 mM MOPS, pH 7.0, 5 mM EDTA, 20 mM NaCl, 5 % glycerol was mixed 1:1 with a cryoprotectant solution containing 35.5 % (w/v) PEG 4000, 0.2 M ammonium acetate, 9 % glycerol, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.875 α = 90 b = 89.842 β = 90 c = 91.556 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 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 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 2.45 35.1 98.7 0.084 6.6 20560 58.3
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) 2.45 2.54 90.4 0.3 4.4 1855
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 PDB entry 2PS0 2.47 35.1 20560 20515 1068 97.97 0.243 0.24 0.2365 0.303 0.2984 RANDOM 58.271
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] 3.69 -5.13 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.999 r_dihedral_angle_4_deg 21.929 r_dihedral_angle_3_deg 16.684 r_dihedral_angle_1_deg 5.479 r_scangle_it 2.152 r_scbond_it 1.366 r_angle_refined_deg 1.341 r_mcangle_it 1.19 r_mcbond_it 0.672 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.999 r_dihedral_angle_4_deg 21.929 r_dihedral_angle_3_deg 16.684 r_dihedral_angle_1_deg 5.479 r_scangle_it 2.152 r_scbond_it 1.366 r_angle_refined_deg 1.341 r_mcangle_it 1.19 r_mcbond_it 0.672 r_nbtor_refined 0.308 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.228 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4066 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
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