3MY9

Crystal structure of a muconate cycloisomerase from Azorhizobium caulinodans


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5294100mM Bis-Tris pH 5.5, 300mM magnesium formate dihydrate, vapor diffusion, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4750.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.993α = 90
b = 127.993β = 90
c = 98.036γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.23099.90.0970.09714.219.52095737.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.241000.5530.553319.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.2202093520893107299.80.2050.2020.254RANDOM58.948
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]
-0.49-0.490.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.841
r_dihedral_angle_4_deg17.179
r_dihedral_angle_3_deg14.666
r_dihedral_angle_1_deg5.826
r_scangle_it3.165
r_scbond_it2.083
r_angle_refined_deg1.381
r_mcangle_it1.312
r_angle_other_deg0.907
r_mcbond_it0.715
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.841
r_dihedral_angle_4_deg17.179
r_dihedral_angle_3_deg14.666
r_dihedral_angle_1_deg5.826
r_scangle_it3.165
r_scbond_it2.083
r_angle_refined_deg1.381
r_mcangle_it1.312
r_angle_other_deg0.907
r_mcbond_it0.715
r_mcbond_other0.152
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.006
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 Atoms2640
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms8

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SHELXCDphasing
SHELXEmodel building