2HZE | pdb_00002hze

Crystal structures of a poxviral glutaredoxin in the oxidized and reduced states show redox-correlated structural changes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KTEPDB ENTRY 1KTE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.62950.1 M NaCacodylate pH 5.2, 12.5% MPD, 10 mM Tris pH 8.0, 50 mM NaCl. Cryo solution containing 0.1 M NaCacodylate pH 5.2, 40% MPD and 50 mM GSH added 5 minutes before flash-freezing., pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1342.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.627α = 90
b = 66.668β = 90
c = 108.096γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1ALS8.3.1

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
11.854.0799.621297212973.971.76
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8797.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1KTE1.819.542129721297106599.680.186790.186790.185680.20.208040.22RANDOM28.305
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.986
r_dihedral_angle_4_deg22.222
r_dihedral_angle_3_deg16.221
r_scangle_it8.611
r_dihedral_angle_1_deg5.971
r_scbond_it5.96
r_angle_other_deg3.61
r_mcangle_it3.311
r_mcbond_it2.066
r_angle_refined_deg1.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.986
r_dihedral_angle_4_deg22.222
r_dihedral_angle_3_deg16.221
r_scangle_it8.611
r_dihedral_angle_1_deg5.971
r_scbond_it5.96
r_angle_other_deg3.61
r_mcangle_it3.311
r_mcbond_it2.066
r_angle_refined_deg1.906
r_chiral_restr0.573
r_symmetry_vdw_other0.337
r_symmetry_hbond_refined0.266
r_nbd_other0.238
r_nbd_refined0.213
r_xyhbond_nbd_refined0.175
r_symmetry_vdw_refined0.142
r_nbtor_other0.107
r_bond_refined_d0.021
r_gen_planes_other0.01
r_gen_planes_refined0.007
r_bond_other_d
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1757
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
CCP4data scaling
XFITdata reduction