3KXR

Structure of the cystathionine beta-synthase pair domain of the putative Mg2+ transporter SO5017 from Shewanella oneidensis MR-1.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.2295PEG3350 25%,di-Na-Tartrate 0.2M,Tris0.1M pH8.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.9257.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.596α = 90
b = 103.596β = 90
c = 134.302γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRROR2009-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9791APS19-ID

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
12.45099.90.0930.09357.07118.51086710867-361.8
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)
12.42.4498.20.8780.8783.618.3537

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.4150108351083551799.590.1910.1910.190.228RANDOM37.37
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]
-1.86-0.93-1.862.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.858
r_dihedral_angle_4_deg21.58
r_dihedral_angle_3_deg16.647
r_dihedral_angle_1_deg5.789
r_scangle_it4.147
r_scbond_it2.603
r_angle_refined_deg1.453
r_mcangle_it1.414
r_angle_other_deg0.906
r_mcbond_it0.695
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.858
r_dihedral_angle_4_deg21.58
r_dihedral_angle_3_deg16.647
r_dihedral_angle_1_deg5.789
r_scangle_it4.147
r_scbond_it2.603
r_angle_refined_deg1.453
r_mcangle_it1.414
r_angle_other_deg0.906
r_mcbond_it0.695
r_mcbond_other0.127
r_chiral_restr0.08
r_bond_refined_d0.017
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1364
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms2

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
ARP/wARPmodel building
CCP4model building
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-2000data scaling
DMphasing
CCP4phasing