3EO8

Crystal structure of BluB-like flavoprotein (YP_001089088.1) from CLOSTRIDIUM DIFFICILE 630 at 1.74 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.627715.0000% Glycerol, 0.1700M NH4OAc, 25.5000% PEG-4000, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2745.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.843α = 90
b = 183.265β = 104.89
c = 74.393γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2008-08-04MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837,0.97918,0.97934SSRLBL9-2

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
11.7448.33797.80.128.64133857-314.167
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)
11.741.896.80.7111.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.7448.337133813674797.860.1590.1560.198RANDOM27.441
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]
0.55-1.2-0.55-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.76
r_dihedral_angle_4_deg12.759
r_dihedral_angle_3_deg12.347
r_dihedral_angle_1_deg5.51
r_scangle_it2.86
r_scbond_it1.965
r_angle_refined_deg1.334
r_mcangle_it1.061
r_angle_other_deg0.898
r_mcbond_it0.767
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.76
r_dihedral_angle_4_deg12.759
r_dihedral_angle_3_deg12.347
r_dihedral_angle_1_deg5.51
r_scangle_it2.86
r_scbond_it1.965
r_angle_refined_deg1.334
r_mcangle_it1.061
r_angle_other_deg0.898
r_mcbond_it0.767
r_symmetry_vdw_other0.24
r_symmetry_vdw_refined0.229
r_nbd_refined0.225
r_mcbond_other0.206
r_nbd_other0.19
r_nbtor_refined0.187
r_symmetry_hbond_refined0.18
r_xyhbond_nbd_refined0.155
r_nbtor_other0.087
r_chiral_restr0.081
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10336
Nucleic Acid Atoms
Solvent Atoms2045
Heterogen Atoms282

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction