1XRE

Crystal Structure of SodA-2 (BA5696) from Bacillus anthracis at 1.8A Resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JR9PDB ENTRY 1JR9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8291PEG 3350, MgCl2, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.242.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.842α = 90
b = 69.866β = 106.85
c = 56.574γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Rh coated Si mirror2004-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.87000SRSPX9.6

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
11.85098.80.07126.333.63773037730
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)
1.81.86940.5971.9433554

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 1JR91.829.09357193571918791000.16170.16170.158720.21932RANDOM27.488
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]
-0.020.09-0.030.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.477
r_dihedral_angle_3_deg15.443
r_dihedral_angle_4_deg12.473
r_sphericity_free6.776
r_dihedral_angle_1_deg6.41
r_scangle_it5.077
r_scbond_it3.957
r_rigid_bond_restr3.293
r_sphericity_bonded2.851
r_mcangle_it2.488
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.477
r_dihedral_angle_3_deg15.443
r_dihedral_angle_4_deg12.473
r_sphericity_free6.776
r_dihedral_angle_1_deg6.41
r_scangle_it5.077
r_scbond_it3.957
r_rigid_bond_restr3.293
r_sphericity_bonded2.851
r_mcangle_it2.488
r_mcbond_it1.883
r_angle_refined_deg1.444
r_angle_other_deg0.91
r_mcbond_other0.697
r_symmetry_hbond_refined0.249
r_symmetry_vdw_other0.227
r_nbd_refined0.213
r_nbtor_refined0.183
r_nbd_other0.182
r_symmetry_vdw_refined0.168
r_xyhbond_nbd_refined0.164
r_chiral_restr0.097
r_nbtor_other0.084
r_bond_refined_d0.015
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3284
Nucleic Acid Atoms
Solvent Atoms374
Heterogen Atoms2

Software

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