3N73

Crystal structure of a putative 4-hydroxy-2-oxoglutarate aldolase from Bacillus cereus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52950.1M BIS-TRIS PH6.5, 0.2M NACL, 25% PEG3350, VAPOR DIFFUSION - HANGING DROP, TEMPERATURE 273K, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3246.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.066α = 90
b = 166.644β = 90
c = 37.279γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRROR2008-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9793APS19-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
12.055099.30.1080.10826.3717.73082030820-331.5
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)
2.052.0966.60.6730.6733.37.21452

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 DIFFRACTIONSADTHROUGHOUT2.07502915129151156196.860.171610.171610.168920.22128RANDOM32.068
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]
-0.660.480.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.718
r_dihedral_angle_4_deg19.409
r_dihedral_angle_3_deg12.692
r_dihedral_angle_1_deg6.145
r_scangle_it3.479
r_scbond_it2.093
r_angle_refined_deg1.441
r_mcangle_it1.159
r_angle_other_deg0.932
r_mcbond_it0.659
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.718
r_dihedral_angle_4_deg19.409
r_dihedral_angle_3_deg12.692
r_dihedral_angle_1_deg6.145
r_scangle_it3.479
r_scbond_it2.093
r_angle_refined_deg1.441
r_mcangle_it1.159
r_angle_other_deg0.932
r_mcbond_it0.659
r_mcbond_other0.196
r_chiral_restr0.084
r_bond_refined_d0.016
r_bond_other_d0.008
r_gen_planes_refined0.007
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 Atoms3775
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms3

Software

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