4MYM

Crystal structure of a glyoxalase/ bleomycin resistance protein/ dioxygenase from Nocardioides


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529325% PEG3350, 0.1M Bis-Tris, 0.2M NaCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3146.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.66α = 90
b = 83.589β = 90
c = 102.413γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9792NSLSX29A

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
11.95099.90.0921113.8148251482520.012
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)
11.91.9699.90.45512.61228

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 DIFFRACTIONSADTHROUGHOUT1.938.03147621401674699.50.2180.187980.186410.21722RANDOM25.849
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]
-0.3-2.152.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.122
r_dihedral_angle_4_deg14.901
r_dihedral_angle_3_deg12.447
r_dihedral_angle_1_deg5.646
r_long_range_B_refined4.411
r_long_range_B_other4.405
r_scangle_other2.985
r_mcangle_other2.179
r_mcangle_it2.175
r_scbond_it1.882
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.122
r_dihedral_angle_4_deg14.901
r_dihedral_angle_3_deg12.447
r_dihedral_angle_1_deg5.646
r_long_range_B_refined4.411
r_long_range_B_other4.405
r_scangle_other2.985
r_mcangle_other2.179
r_mcangle_it2.175
r_scbond_it1.882
r_scbond_other1.881
r_mcbond_it1.324
r_mcbond_other1.308
r_angle_refined_deg1.256
r_angle_other_deg0.737
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms1183
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms14

Software

Software
Software NamePurpose
CBASSdata collection
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling