1XKY

Crystal Structure of Dihydrodipicolinate Synthase DapA-2 (BA3935) from Bacillus Anthracis at 1.94A Resolution.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8291PEG 5000 MME, KSCN, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.203α = 90
b = 126.882β = 90
c = 173.319γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCHmultilayer optics2004-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54189

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
11.942095.60.08217.25.4871188711829.2
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)
1.942.0184.70.31533.47624

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-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DHP1.9419.96870048264443601000.155550.155550.15340.19719RANDOM16.158
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]
0.03-0.110.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.614
r_dihedral_angle_4_deg14.395
r_dihedral_angle_3_deg12.939
r_dihedral_angle_1_deg5.642
r_scangle_it2.67
r_scbond_it1.532
r_angle_refined_deg1.183
r_angle_other_deg0.898
r_mcangle_it0.839
r_mcbond_it0.433
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.614
r_dihedral_angle_4_deg14.395
r_dihedral_angle_3_deg12.939
r_dihedral_angle_1_deg5.642
r_scangle_it2.67
r_scbond_it1.532
r_angle_refined_deg1.183
r_angle_other_deg0.898
r_mcangle_it0.839
r_mcbond_it0.433
r_nbd_refined0.229
r_symmetry_vdw_other0.191
r_nbtor_refined0.165
r_nbd_other0.164
r_symmetry_vdw_refined0.162
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_refined0.132
r_metal_ion_refined0.099
r_chiral_restr0.095
r_mcbond_other0.087
r_nbtor_other0.079
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8758
Nucleic Acid Atoms
Solvent Atoms1748
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing