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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X74 PDB ENTRY 1X74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 1.52M Ammonium phosphate, 10mM Barium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.71 54.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.95 α = 90 b = 79.58 β = 90.07 c = 117.43 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH mirrors 2005-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.54179
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.85 35 95 0.074 0.074 13.5 4.5 134349 27.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.9 84.2 0.492 2.7 9101
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1X74 1.85 19.58 127524 127524 6719 94.97 0.20461 0.20238 0.202 0.2273 0.24644 0.2473 RANDOM 30.477
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.719 r_dihedral_angle_4_deg 15.804 r_dihedral_angle_3_deg 15.247 r_dihedral_angle_1_deg 5.839 r_scangle_it 2.567 r_scbond_it 1.729 r_angle_refined_deg 1.427 r_mcangle_it 1.12 r_mcbond_it 0.713 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.719 r_dihedral_angle_4_deg 15.804 r_dihedral_angle_3_deg 15.247 r_dihedral_angle_1_deg 5.839 r_scangle_it 2.567 r_scbond_it 1.729 r_angle_refined_deg 1.427 r_mcangle_it 1.12 r_mcbond_it 0.713 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.253 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10748 Nucleic Acid Atoms Solvent Atoms 1106 Heterogen Atoms 496
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing