5D00

Crystal structure of BshA from B. subtilis complexed with N-acetylglucosaminyl-malate and UMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MBO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72982% (v/v) tascimate, 6% (w/v) PEG-3400, 25 mM NaCl, 10 mM HEPES, 5 mM UDP-N-acetylglucosamine
Crystal Properties
Matthews coefficientSolvent content
2.1643.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.66α = 90
b = 164.627β = 90
c = 97.729γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.078APS21-ID-D

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
12.1593.731000.093159.640122
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)
12.152.271000.693.79.9

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 REPLACEMENTTHROUGHOUT3MBO2.1582.3138084201099.960.18680.18430.2341RANDOM41.659
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]
-0.15-0.260.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.569
r_dihedral_angle_4_deg18.877
r_dihedral_angle_3_deg15.324
r_dihedral_angle_1_deg6.809
r_mcangle_it4.972
r_mcbond_it3.475
r_mcbond_other3.462
r_angle_refined_deg1.823
r_angle_other_deg0.841
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.569
r_dihedral_angle_4_deg18.877
r_dihedral_angle_3_deg15.324
r_dihedral_angle_1_deg6.809
r_mcangle_it4.972
r_mcbond_it3.475
r_mcbond_other3.462
r_angle_refined_deg1.823
r_angle_other_deg0.841
r_chiral_restr0.102
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5555
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms72

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
XDSdata scaling
Cootmodel building