4LSB

Crystal structure of a putative lyase/mutase from Burkholderia cenocepacia J2315


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZE3PDB entry 2ZE3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.528920% PEG 8000, 0.2M MgCl2, Tris HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1342.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.06α = 90
b = 70.03β = 90
c = 141.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9798APS21-ID-F

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
11.85097.20.06418.654851814.3
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)
11.81.8598.50.4663.34.973583

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 2ZE31.847.3345828244096.80.168950.166740.21081RANDOM22.274
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]
3.16-1.39-1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.325
r_dihedral_angle_4_deg15.041
r_dihedral_angle_3_deg12.392
r_dihedral_angle_1_deg5.708
r_long_range_B_refined4.951
r_long_range_B_other4.769
r_scangle_other2.882
r_mcangle_other2.065
r_mcangle_it2.064
r_scbond_it1.881
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.325
r_dihedral_angle_4_deg15.041
r_dihedral_angle_3_deg12.392
r_dihedral_angle_1_deg5.708
r_long_range_B_refined4.951
r_long_range_B_other4.769
r_scangle_other2.882
r_mcangle_other2.065
r_mcangle_it2.064
r_scbond_it1.881
r_scbond_other1.878
r_angle_refined_deg1.568
r_mcbond_it1.338
r_mcbond_other1.334
r_angle_other_deg0.852
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3986
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms4

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling