3N2X

Crystal structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12 in complex with pyruvate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V8Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.5298100mM HEPES pH 6.5, 200mM MgCl2, 25% PEG 3350, Microbatch, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.13α = 90
b = 153.55β = 90
c = 55.53γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.973ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.248.97599.30.1020.1116.9362107-322.397
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.25960.3390.375.9

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 REPLACEMENTTHROUGHOUT2V8Z2.248.9756210731061000.1810.1790.222RANDOM13.778
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]
-1.320.670.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.501
r_dihedral_angle_4_deg19.002
r_dihedral_angle_3_deg15.223
r_dihedral_angle_1_deg6.064
r_scangle_it3.906
r_scbond_it2.53
r_angle_refined_deg1.866
r_mcangle_it1.375
r_mcbond_it0.772
r_chiral_restr0.189
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.501
r_dihedral_angle_4_deg19.002
r_dihedral_angle_3_deg15.223
r_dihedral_angle_1_deg6.064
r_scangle_it3.906
r_scbond_it2.53
r_angle_refined_deg1.866
r_mcangle_it1.375
r_mcbond_it0.772
r_chiral_restr0.189
r_bond_refined_d0.023
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9055
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms16

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction