2GCE

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
2.7154.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 179.95α = 90
b = 79.58β = 90.07
c = 117.43γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHmirrors2005-08-10MSINGLE 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
11.8535950.0740.07413.54.513434927.8
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)
1.851.984.20.4922.79101

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 1X741.8519.58127524127524671994.970.204610.202380.2020.24644RANDOM30.477
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_deg32.719
r_dihedral_angle_4_deg15.804
r_dihedral_angle_3_deg15.247
r_dihedral_angle_1_deg5.839
r_scangle_it2.567
r_scbond_it1.729
r_angle_refined_deg1.427
r_mcangle_it1.12
r_mcbond_it0.713
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.719
r_dihedral_angle_4_deg15.804
r_dihedral_angle_3_deg15.247
r_dihedral_angle_1_deg5.839
r_scangle_it2.567
r_scbond_it1.729
r_angle_refined_deg1.427
r_mcangle_it1.12
r_mcbond_it0.713
r_nbtor_refined0.312
r_symmetry_hbond_refined0.253
r_symmetry_vdw_refined0.241
r_nbd_refined0.208
r_xyhbond_nbd_refined0.177
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10748
Nucleic Acid Atoms
Solvent Atoms1106
Heterogen Atoms496

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
MOLREPphasing