6N7F

1.90 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus pyogenes in Complex with FAD.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V36 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5292Protein: 9.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 1mM FAD; Screen: Classics II (F10), 0.2M Sodium chloride, 0.1M Bis-Tris pH=5.5, 25% (w/v) PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.5451.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.4α = 67.13
b = 86.65β = 74.15
c = 86.67γ = 74.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9786APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)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
11.93097.70.0690.0690.0910.058122.3148744-323
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9394.90.5170.5170.6810.4390.6571.72.3

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 REPLACEMENTTHROUGHOUT5V361.929.47141509723297.520.1710.168960.21042RANDOM26.814
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]
0.41-0.32-0.33-0.2-0.05-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.273
r_dihedral_angle_4_deg10.818
r_dihedral_angle_3_deg9.817
r_long_range_B_refined5.176
r_long_range_B_other4.938
r_dihedral_angle_1_deg3.506
r_scangle_other2.592
r_scbond_it1.649
r_scbond_other1.649
r_mcangle_it1.537
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.273
r_dihedral_angle_4_deg10.818
r_dihedral_angle_3_deg9.817
r_long_range_B_refined5.176
r_long_range_B_other4.938
r_dihedral_angle_1_deg3.506
r_scangle_other2.592
r_scbond_it1.649
r_scbond_other1.649
r_mcangle_it1.537
r_mcangle_other1.537
r_angle_refined_deg1.41
r_mcbond_it0.975
r_mcbond_other0.974
r_angle_other_deg0.377
r_chiral_restr0.064
r_gen_planes_refined0.055
r_gen_planes_other0.051
r_bond_refined_d0.006
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 Atoms13806
Nucleic Acid Atoms
Solvent Atoms1708
Heterogen Atoms320

Software

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