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Crystal structure of propionyl-CoA carboxylase, beta subunit (TM0716) from THERMOTOGA MARITIMA at 2.30 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ON3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 6 277 0.2M Li2SO4, 35.0% MPD, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.46 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.922 α = 90 b = 162.21 β = 90 c = 187.117 γ = 90
Symmetry Space Group P 21 21 21
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 APS double crystal, Rosenbaum-Rock vertical focusing mirror 2003-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.3 45.36 96.76 0.124 11.58 7.19 148537 41.19
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 2.3 2.38 84.38 0.553 1.32 2.82 12848
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1ON3 2.3 45.36 141028 7428 96.56 0.15681 0.154 0.1647 0.2098 0.2153 RANDOM 29.088
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] 1.06 0.48 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.909 r_dihedral_angle_4_deg 17.103 r_dihedral_angle_3_deg 15.044 r_dihedral_angle_1_deg 6.089 r_scangle_it 5.998 r_scbond_it 4.408 r_mcangle_it 2.221 r_mcbond_it 1.791 r_angle_refined_deg 1.445 r_angle_other_deg 0.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.909 r_dihedral_angle_4_deg 17.103 r_dihedral_angle_3_deg 15.044 r_dihedral_angle_1_deg 6.089 r_scangle_it 5.998 r_scbond_it 4.408 r_mcangle_it 2.221 r_mcbond_it 1.791 r_angle_refined_deg 1.445 r_angle_other_deg 0.842 r_mcbond_other 0.527 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.195 r_symmetry_vdw_other 0.184 r_metal_ion_refined 0.179 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.115 r_nbtor_other 0.086 r_chiral_restr 0.079 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23567 Nucleic Acid Atoms Solvent Atoms 1439 Heterogen Atoms 43
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement