2PS3

Structure and metal binding properties of ZnuA, a periplasmic zinc transporter from Escherichia coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PS0PDB entry 2PS0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62935 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 coefficientSolvent content
2.2745.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.875α = 90
b = 89.842β = 90
c = 91.556γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm platemirrors2006-07-06MSINGLE WAVELENGTH
21
31
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 5ID-BAPS5ID-B
2SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID
3SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4535.198.70.0846.62056058.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.452.5490.40.34.41855

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2PS02.4735.12056020515106897.970.2430.240.303RANDOM58.271
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]
3.69-5.131.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.999
r_dihedral_angle_4_deg21.929
r_dihedral_angle_3_deg16.684
r_dihedral_angle_1_deg5.479
r_scangle_it2.152
r_scbond_it1.366
r_angle_refined_deg1.341
r_mcangle_it1.19
r_mcbond_it0.672
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.999
r_dihedral_angle_4_deg21.929
r_dihedral_angle_3_deg16.684
r_dihedral_angle_1_deg5.479
r_scangle_it2.152
r_scbond_it1.366
r_angle_refined_deg1.341
r_mcangle_it1.19
r_mcbond_it0.672
r_nbtor_refined0.308
r_nbd_refined0.231
r_symmetry_vdw_refined0.228
r_xyhbond_nbd_refined0.15
r_symmetry_hbond_refined0.14
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4066
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction