1XL9

Crystal Structure of Dihydrodipicolinate Synthase DapA-2 (BA3935) from Bacillus Anthracis.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XKY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5291PEG 3350, NaFormate, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.957.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.463α = 90
b = 126.564β = 90
c = 134.636γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Mirror2004-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.20.97600SRSPX14.2

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
12.235099.80.11725.136.17436574365
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)
2.232.3199.10.515.494.57299

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 REPLACEMENTTHROUGHOUT1XKY2.2346.13677506775036091000.19720.19720.194080.25432RANDOM40.581
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]
0.30.25-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.047
r_dihedral_angle_4_deg18.602
r_dihedral_angle_3_deg18.555
r_dihedral_angle_1_deg6.752
r_scangle_it3.267
r_scbond_it2.093
r_angle_refined_deg1.69
r_mcangle_it1.201
r_mcbond_it1.014
r_angle_other_deg0.917
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.047
r_dihedral_angle_4_deg18.602
r_dihedral_angle_3_deg18.555
r_dihedral_angle_1_deg6.752
r_scangle_it3.267
r_scbond_it2.093
r_angle_refined_deg1.69
r_mcangle_it1.201
r_mcbond_it1.014
r_angle_other_deg0.917
r_symmetry_vdw_other0.275
r_nbd_refined0.215
r_xyhbond_nbd_refined0.192
r_nbd_other0.179
r_mcbond_other0.174
r_nbtor_refined0.172
r_symmetry_hbond_refined0.149
r_symmetry_vdw_refined0.128
r_chiral_restr0.097
r_nbtor_other0.088
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
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 Atoms8776
Nucleic Acid Atoms
Solvent Atoms759
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing