3P0X

Crystal structure of isocitrate lyase from Brucella melitensis, bound to magnesium isocitrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OQ8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6290Internal tracking number 217292B10. Protein (26 mg/mL) and PACT Screen condition B10: 0.2 M MgCl2, 20% PEG6000, 0.1 M MES pH 6.0, 5 mM isocitrate, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.5251.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.91α = 90
b = 135.93β = 90
c = 181.79γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.541780

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
12.3547.699.80.10112.133.88013479958-328.906
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)
12.352.4199.20.56322.95866

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 REPLACEMENTTHROUGHOUT3OQ82.3547.68013479682399199.460.180.180.1780.23RANDOM22.264
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]
1.12-0.38-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.778
r_dihedral_angle_4_deg17.585
r_dihedral_angle_3_deg14.061
r_dihedral_angle_1_deg5.671
r_scangle_it2.34
r_scbond_it1.417
r_angle_refined_deg1.246
r_angle_other_deg0.879
r_mcangle_it0.818
r_mcbond_it0.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.778
r_dihedral_angle_4_deg17.585
r_dihedral_angle_3_deg14.061
r_dihedral_angle_1_deg5.671
r_scangle_it2.34
r_scbond_it1.417
r_angle_refined_deg1.246
r_angle_other_deg0.879
r_mcangle_it0.818
r_mcbond_it0.431
r_mcbond_other0.113
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12879
Nucleic Acid Atoms
Solvent Atoms687
Heterogen Atoms80

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction