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The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an asparte/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 2.75 55.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.7 α = 90 b = 79.81 β = 89.93 c = 118.06 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 1.6 35 97 0.063 0.063 15 4.8 214258 26
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 1.6 1.8 94 0.274 61537
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 1.6 19.83 203330 203330 10825 96.99 0.21186 0.21015 0.21 0.2439 0.24413 0.2546 RANDOM 28.417
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 32.773 r_dihedral_angle_4_deg 16.348 r_dihedral_angle_3_deg 14.776 r_dihedral_angle_1_deg 5.764 r_scangle_it 3.062 r_scbond_it 2.159 r_angle_refined_deg 1.557 r_mcangle_it 1.408 r_mcbond_it 0.977 r_symmetry_vdw_refined 0.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.773 r_dihedral_angle_4_deg 16.348 r_dihedral_angle_3_deg 14.776 r_dihedral_angle_1_deg 5.764 r_scangle_it 3.062 r_scbond_it 2.159 r_angle_refined_deg 1.557 r_mcangle_it 1.408 r_mcbond_it 0.977 r_symmetry_vdw_refined 0.365 r_nbtor_refined 0.312 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10716 Nucleic Acid Atoms Solvent Atoms 1208 Heterogen Atoms 273
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing