2DVZ

Structure of a periplasmic transporter


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.32770.1M CdCl2, 0.1M sodium acetate, 30-32% (v/v) PEG 400 or 34-40% (v/v) PEG 200, pH 4.30, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.652.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.829α = 90
b = 53.829β = 90
c = 422.66γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.31596.60.0796915977
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)
2.32.36720.1255.38.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.315159771597786396.610.180.180130.176330.24924RANDOM18.349
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]
0.050.020.05-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.437
r_dihedral_angle_4_deg19.127
r_dihedral_angle_3_deg15.607
r_sphericity_free7.428
r_dihedral_angle_1_deg6.445
r_scangle_it4.06
r_scbond_it2.716
r_sphericity_bonded2.686
r_rigid_bond_restr1.716
r_angle_refined_deg1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.437
r_dihedral_angle_4_deg19.127
r_dihedral_angle_3_deg15.607
r_sphericity_free7.428
r_dihedral_angle_1_deg6.445
r_scangle_it4.06
r_scbond_it2.716
r_sphericity_bonded2.686
r_rigid_bond_restr1.716
r_angle_refined_deg1.61
r_mcangle_it1.598
r_mcbond_it1.008
r_symmetry_hbond_refined0.499
r_nbtor_refined0.301
r_symmetry_vdw_refined0.287
r_metal_ion_refined0.229
r_xyhbond_nbd_refined0.221
r_nbd_refined0.209
r_chiral_restr0.099
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2248
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
CCP4data scaling
SHELXSphasing