2GD0

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
2.7455.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 215.74α = 90
b = 79.75β = 123.14
c = 117.92γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBent mirror2005-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.00MAX III911-3

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
11.73597.20.0530.05314.23.817915626.2
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)
11.71.896.40.2934.827907

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 1X741.719.8170143170143894697.40.237780.2360.235780.27554RANDOM28.421
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_deg31.876
r_dihedral_angle_3_deg14.769
r_dihedral_angle_4_deg14.647
r_dihedral_angle_1_deg6.063
r_scangle_it3.269
r_scbond_it2.352
r_angle_refined_deg1.659
r_mcangle_it1.631
r_mcbond_it1.097
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.876
r_dihedral_angle_3_deg14.769
r_dihedral_angle_4_deg14.647
r_dihedral_angle_1_deg6.063
r_scangle_it3.269
r_scbond_it2.352
r_angle_refined_deg1.659
r_mcangle_it1.631
r_mcbond_it1.097
r_nbtor_refined0.312
r_symmetry_vdw_refined0.22
r_nbd_refined0.218
r_xyhbond_nbd_refined0.177
r_symmetry_hbond_refined0.167
r_chiral_restr0.108
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10716
Nucleic Acid Atoms
Solvent Atoms1380
Heterogen Atoms280

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
MOLREPphasing