3LWB

Crystal Structure of apo D-alanine:D-alanine Ligase (Ddl) from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I87homology model derived from PDB ENTRY 2I87

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293Well solution consisted of 20% PEG 3350, 0.1M potassium nitrate. 1uL of well solution was mixed with 1uL protein solution (10mg/mL) and equilibrated over 500uL well solution., pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.72α = 90
b = 108.302β = 99.92
c = 69.064γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2004-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.96411APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.12093.90.0520.05210.53.6409574095734.16
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1784.90.4060.4062.73.13686

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUThomology model derived from PDB ENTRY 2I872.119.2033875838758189688.750.1730.221random45.294
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]
-0.401-0.4040.82-0.42
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d9.793
f_nbd_refined4.063
f_angle_d0.622
f_chiral_restr0.046
f_bond_d0.004
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4510
Nucleic Acid Atoms
Solvent Atoms383
Heterogen Atoms8

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection