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Crystal structure of CaiB, a type III CoA transferase in carnitine metabolism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XA3 PDB entry 1XA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 PEG 3350, Ammonium Sulphate, Glycerol, Sodium Chloride, Bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.595 α = 90 b = 125.668 β = 108.96 c = 69.963 γ = 90
Symmetry Space Group P 1 21 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 2004-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.09 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 30 98.9 0.067 7.71 3.95 70549 70549 -3 19.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 95.5 0.23 3.01 3.7
Refinement Statistics Diffraction ID Structure Solution 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 PDB entry 1XA3 1.9 30 66935 66935 3581 98.83 0.14528 0.14528 0.14363 0.1579 0.17554 0.1882 RANDOM 19.01
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] 0.06 0.54 0.2 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.976 r_scangle_it 4.238 r_scbond_it 2.752 r_mcangle_it 1.564 r_angle_refined_deg 1.459 r_angle_other_deg 0.844 r_mcbond_it 0.841 r_nbd_other 0.244 r_symmetry_vdw_other 0.221 r_nbd_refined 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.976 r_scangle_it 4.238 r_scbond_it 2.752 r_mcangle_it 1.564 r_angle_refined_deg 1.459 r_angle_other_deg 0.844 r_mcbond_it 0.841 r_nbd_other 0.244 r_symmetry_vdw_other 0.221 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.09 r_nbtor_other 0.085 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6254 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing