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Dynamic domains of Succinyl-CoA:3-ketoacid-coenzyme A transferase from pig heart.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O9L PDB ENTRY 1O9L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 4 ul Well Solution: 18-22% PEG 3350 or 4000, 75 mM Tris/HCl pH 8. 4 ul Protein solution: 10-15 mg/ml protein, 20 mM MOPS pH 7.2, 1 mM EDTA, 1 mM DTT, 0.2 mM PMSF, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.715 α = 90 b = 133.566 β = 104.98 c = 102.23 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 MAR CCD 130 mm 1998-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.948 ESRF ID14-3
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 1.5 20 97.7 0.042 0.042 12 3.3 297163 297163 17.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 82 0.296 0.296 2.3 2.2 18372
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 1O9L 1.5 20 296782 296782 14899 97.6 0.1657 0.1657 0.16502 0.1729 0.18538 0.1921 RANDOM 19.924
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] 0.92 0.15 -0.76 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.68 r_dihedral_angle_4_deg 13.902 r_dihedral_angle_3_deg 12.414 r_dihedral_angle_1_deg 6.206 r_angle_other_deg 4.206 r_scangle_it 3.231 r_scbond_it 2.315 r_angle_refined_deg 1.528 r_mcangle_it 1.208 r_mcbond_it 1.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.68 r_dihedral_angle_4_deg 13.902 r_dihedral_angle_3_deg 12.414 r_dihedral_angle_1_deg 6.206 r_angle_other_deg 4.206 r_scangle_it 3.231 r_scbond_it 2.315 r_angle_refined_deg 1.528 r_mcangle_it 1.208 r_mcbond_it 1.114 r_symmetry_vdw_other 0.304 r_nbd_other 0.242 r_mcbond_other 0.23 r_nbd_refined 0.22 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.152 r_nbtor_other 0.111 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14137 Nucleic Acid Atoms Solvent Atoms 1581 Heterogen Atoms 14
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling