3OCE

Crystal structure of fumarate lyase:delta crystallin from Brucella melitensis bound to cobalt


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JSWPDB entry 1jsw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.528946.3 mg/mL BrabA.00047.a.A6 PS00513 against JCSG+ condition G3, 10 mM CoCl2, 0.1 M Tris, 20% polyvinyl pyrrolidone K15 with 20% ethylene glycol as cryo-protectant, crsytal tracking ID 215219g3, 3C protease cleaved, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.1460.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.33α = 90
b = 113.55β = 90
c = 236.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
12.585099.10.14610.037.18164480944-329.903
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)
2.582.65990.5653.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1jsw2.585080691405498.850.19840.19590.2454RANDOM29.6871
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]
-1.65-0.061.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.22
r_dihedral_angle_3_deg18.128
r_dihedral_angle_4_deg17.4
r_dihedral_angle_1_deg5.793
r_scangle_it3.558
r_scbond_it1.999
r_angle_refined_deg1.538
r_mcangle_it1.227
r_mcbond_it0.624
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.22
r_dihedral_angle_3_deg18.128
r_dihedral_angle_4_deg17.4
r_dihedral_angle_1_deg5.793
r_scangle_it3.558
r_scbond_it1.999
r_angle_refined_deg1.538
r_mcangle_it1.227
r_mcbond_it0.624
r_chiral_restr0.104
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13775
Nucleic Acid Atoms
Solvent Atoms544
Heterogen Atoms20

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction