5VDN

1.55 Angstrom Resolution Crystal Structure of Glutathione Reductase from Yersinia pestis in Complex with FAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GES 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3295Protein: 10.0 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: Classics II (B6), 0.49M Sodium phosphate, 0.91M Potassium phosphate; Cryo: Screen : 50% Sucrose (1:1)
Crystal Properties
Matthews coefficientSolvent content
2.7355

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.844α = 90
b = 125.844β = 90
c = 124.557γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rpim I (All)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
11.55301000.060.060.02525.36.3161196-319.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.581000.7210.7210.3190.7292.36

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1GES1.5529.94153253789599.820.145670.144710.16456RANDOM20.379
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]
0.070.030.07-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.866
r_dihedral_angle_3_deg9.136
r_dihedral_angle_4_deg8.626
r_long_range_B_refined5.852
r_long_range_B_other5.356
r_dihedral_angle_1_deg3.749
r_scangle_other2.893
r_scbond_it1.866
r_scbond_other1.866
r_angle_refined_deg1.508
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.866
r_dihedral_angle_3_deg9.136
r_dihedral_angle_4_deg8.626
r_long_range_B_refined5.852
r_long_range_B_other5.356
r_dihedral_angle_1_deg3.749
r_scangle_other2.893
r_scbond_it1.866
r_scbond_other1.866
r_angle_refined_deg1.508
r_mcangle_it1.353
r_mcangle_other1.353
r_angle_other_deg0.873
r_mcbond_it0.862
r_mcbond_other0.862
r_chiral_restr0.093
r_gen_planes_refined0.023
r_gen_planes_other0.019
r_bond_refined_d0.009
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6870
Nucleic Acid Atoms
Solvent Atoms1272
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing