2ZDQ

Crystal structure of D-Alanine:D-Alanine Ligase with ATP and D-Alanine:D-Alanine from Thermus thermophius HB8


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92930.91M K2 H Phosphate, 0.49M Na H2 Phosphate, 20% Glycerol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1260.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.052α = 90
b = 95.052β = 90
c = 192.009γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDA fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium.2007-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.0SPring-8BL26B2

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
12.35099.60.0870.0734.817.3399483977131.8
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)
2.32.3896.20.3880.3263.658.93776

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 REPLACEMENTTHROUGHOUT2ZDG2.34837945382894.90.2310.2310.266RANDOM41.2
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]
7.177.17-14.34
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.1
c_improper_angle_d3.7
c_angle_deg2.2
c_bond_d0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4906
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms84

Software

Software
Software NamePurpose
CNSrefinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing