3EU3

Crystal Structure of BdbD from Bacillus subtilis (reduced)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.527% PEG2000, 0.1M ammonium acetate, 0.1M MES, pH6.5, 1mM DTT,cryo-protected with 20% Ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
1.935.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.774α = 90
b = 43.399β = 107.4
c = 54.658γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.528.2197.80.052153.5274502745011
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.5889.50.2673.42.927450

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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.526.082621126211138598.830.187760.186080.180.219190.22RANDOM18.639
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]
0.26-0.050.9-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.327
r_dihedral_angle_3_deg14.006
r_dihedral_angle_1_deg5.251
r_sphericity_free4.729
r_sphericity_bonded3.612
r_scangle_it3.286
r_scbond_it2.211
r_dihedral_angle_4_deg1.856
r_mcangle_it1.605
r_rigid_bond_restr1.361
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1538
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms5

Software

Software
Software NamePurpose
ADSCdata collection
BP3model building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
BP3phasing