2GD6

The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X74PDB ENTRY 1X74

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72941.52M Ammonium phosphate, 10mM Barium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.7655.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.91α = 90
b = 79.94β = 91.03
c = 118.39γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirror2004-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE1.54179

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
12.053594.60.0850.08513.84.610033922.4
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)
12.052.165.90.3043.94845

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 ENTRY 1X742.319.717051670516371398.80.221770.219220.2190.26964RANDOM36.377
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
r_dihedral_angle_2_deg34.558
r_dihedral_angle_4_deg17.554
r_dihedral_angle_3_deg16.266
r_dihedral_angle_1_deg5.67
r_scangle_it2.222
r_scbond_it1.524
r_angle_refined_deg1.398
r_mcangle_it0.747
r_mcbond_it0.458
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.558
r_dihedral_angle_4_deg17.554
r_dihedral_angle_3_deg16.266
r_dihedral_angle_1_deg5.67
r_scangle_it2.222
r_scbond_it1.524
r_angle_refined_deg1.398
r_mcangle_it0.747
r_mcbond_it0.458
r_nbtor_refined0.308
r_symmetry_hbond_refined0.255
r_nbd_refined0.212
r_symmetry_vdw_refined0.21
r_xyhbond_nbd_refined0.189
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10716
Nucleic Acid Atoms
Solvent Atoms672
Heterogen Atoms216

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
MOLREPphasing