2HAY

The Crystal Structure of the Putative NAD(P)H-Flavin Oxidoreductase from Streptococcus pyogenes M1 GAS


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52820.2M Ammonium Sulfate 0.1M MES pH 6.5 30% PEG 5000 MME and Flavin, VAPOR DIFFUSION, SITTING DROP, temperature 282K
Crystal Properties
Matthews coefficientSolvent content
2.3447.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.205α = 90
b = 91.874β = 90
c = 175.693γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2006-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97937APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.115096.20.1389.285806655236
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.112.1973.50.434.045.8

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 DIFFRACTIONSADTHROUGHOUT2.1140.714957949579555296.840.180340.180340.174560.23246RANDOM31.724
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]
3.6-1.97-1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.847
r_dihedral_angle_3_deg18.873
r_dihedral_angle_4_deg16.663
r_dihedral_angle_1_deg5.98
r_scangle_it3.145
r_scbond_it2.033
r_angle_refined_deg1.434
r_mcangle_it1.239
r_mcbond_it0.684
r_symmetry_vdw_refined0.272
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.847
r_dihedral_angle_3_deg18.873
r_dihedral_angle_4_deg16.663
r_dihedral_angle_1_deg5.98
r_scangle_it3.145
r_scbond_it2.033
r_angle_refined_deg1.434
r_mcangle_it1.239
r_mcbond_it0.684
r_symmetry_vdw_refined0.272
r_nbd_refined0.216
r_symmetry_hbond_refined0.209
r_xyhbond_nbd_refined0.159
r_chiral_restr0.109
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7049
Nucleic Acid Atoms
Solvent Atoms609
Heterogen Atoms149

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building