4H2H

Crystal structure of an enolase (mandalate racemase subgroup, target EFI-502101) from Pelagibaca bermudensis htcc2601, with bound mg and l-4-hydroxyproline betaine (betonicine)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PMQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5298Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 10% glycerol, 50 mM MgCl2, 5 mM EDTA, 2 mM NiCl2; Reservoir (0.1 M HEPES:NaOH pH 7.5 70% (v/v) MPD); Soak 2 minutes in (Reservoir + 50 mM MgCl2, 200 mM 4-OH Proline Betaine ) Cryoprotection (Soaking solution), sitting drop vapor diffuction, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3347.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.035α = 90
b = 152.824β = 105.2
c = 113.027γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2012-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7109.07299.90.0858.93.8325934
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)
11.71.7999.90.5770.5771.33.6

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2PMQ1.725.683257873257871643499.90.160.1590.19223.53
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.802
f_angle_d1.109
f_chiral_restr0.074
f_bond_d0.011
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22160
Nucleic Acid Atoms
Solvent Atoms2066
Heterogen Atoms183

Software

Software
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing