3NO1

Crystal Structure of Mandelate racemase/muconate lactonizing enzyme from a Marine actinobacterium in complex with magnesium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MSYPDB ID: 3MSY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52920.2M Magnesium Chloride 0.1M Hepes pH 7.5, 20% PEG 3350, 0.025M ethylenediamine-tetraacetic disodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.1342.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.961α = 115.8
b = 90.103β = 109.75
c = 94.66γ = 97.58
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2010-06-18MSINGLE 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
12.165098.10.08419.10.911778811778811.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.162.2496.60.1910.83.911562

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 REPLACEMENTTHROUGHOUTPDB ID: 3MSY2.1642.511155581155584670960.2120.2070.2070.24RANDOM21.7
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]
4.550.193.19-2.89-0.43-1.66
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_degree22.3
c_angle_deg1.4
c_improper_angle_deg0.82
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16538
Nucleic Acid Atoms
Solvent Atoms626
Heterogen Atoms6

Software

Software
Software NamePurpose
CBASSdata collection
MOLREPphasing
CNSrefinement
DENZOdata reduction
HKL-2000data scaling