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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 2.74 55.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 215.74 α = 90 b = 79.75 β = 123.14 c = 117.92 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 CCD MARRESEARCH Bent mirror 2005-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.00 MAX II I911-3
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 35 97.2 0.053 0.053 14.2 3.8 179156 26.2
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 1.7 1.8 96.4 0.293 4.8 27907
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 1.7 19.8 170143 170143 8946 97.4 0.23778 0.236 0.23578 0.2189 0.27554 0.2555 RANDOM 28.421
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.876 r_dihedral_angle_3_deg 14.769 r_dihedral_angle_4_deg 14.647 r_dihedral_angle_1_deg 6.063 r_scangle_it 3.269 r_scbond_it 2.352 r_angle_refined_deg 1.659 r_mcangle_it 1.631 r_mcbond_it 1.097 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.876 r_dihedral_angle_3_deg 14.769 r_dihedral_angle_4_deg 14.647 r_dihedral_angle_1_deg 6.063 r_scangle_it 3.269 r_scbond_it 2.352 r_angle_refined_deg 1.659 r_mcangle_it 1.631 r_mcbond_it 1.097 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.177 r_symmetry_hbond_refined 0.167 r_chiral_restr 0.108 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10716 Nucleic Acid Atoms Solvent Atoms 1380 Heterogen Atoms 280
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing