2HZL

Crystal structures of a sodium-alpha-keto acid binding subunit from a TRAP transporter in its closed forms


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HZK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.4293100mM sodium citrate 1.4M ammonium sulfate 30mM pyruvate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.021α = 90
b = 78.057β = 124.98
c = 95.139γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97565ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4489913740013731811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4197.9

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2HZK1.439.0113740013731669081000.1730.1730.1730.184RANDOM11.164
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]
0.02-0.060.01-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.896
r_dihedral_angle_3_deg12.769
r_dihedral_angle_4_deg12.748
r_dihedral_angle_1_deg5.762
r_scangle_it2.761
r_scbond_it1.701
r_angle_refined_deg1.143
r_mcangle_it1.038
r_mcbond_it0.537
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.896
r_dihedral_angle_3_deg12.769
r_dihedral_angle_4_deg12.748
r_dihedral_angle_1_deg5.762
r_scangle_it2.761
r_scbond_it1.701
r_angle_refined_deg1.143
r_mcangle_it1.038
r_mcbond_it0.537
r_nbtor_refined0.312
r_nbd_refined0.206
r_symmetry_vdw_refined0.183
r_xyhbond_nbd_refined0.115
r_symmetry_hbond_refined0.107
r_chiral_restr0.079
r_metal_ion_refined0.051
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5304
Nucleic Acid Atoms
Solvent Atoms471
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing