3I4E

Crystal structure of Isocitrate Lyase from Burkholderia pseudomallei


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IGWPDB entry 1IGW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.829324% PEG 1500, 100 MM MES, PROTEIN CONCENTRATION 22MG/ML, PH 5.8, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2144.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.666α = 90
b = 137.025β = 90
c = 160.162γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002008-06-19SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

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
12.6948.9199.70.1445.86.748029
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)
2.72.897.90.665.2

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 1IGW2.6948.914795924260.2160.2130.277RANDOM31.2
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]
-1.22.86-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.812
r_dihedral_angle_3_deg15.073
r_dihedral_angle_4_deg13.746
r_dihedral_angle_1_deg5.108
r_scangle_it1.146
r_angle_refined_deg1.019
r_angle_other_deg0.815
r_scbond_it0.671
r_mcangle_it0.577
r_mcbond_it0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.812
r_dihedral_angle_3_deg15.073
r_dihedral_angle_4_deg13.746
r_dihedral_angle_1_deg5.108
r_scangle_it1.146
r_angle_refined_deg1.019
r_angle_other_deg0.815
r_scbond_it0.671
r_mcangle_it0.577
r_mcbond_it0.308
r_mcbond_other0.056
r_chiral_restr0.055
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 Atoms12580
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement