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Structural analysis of an archaeal lipoylation system. A bi-partite lipoate protein ligase and its E2 lipoyl domain from Thermoplasma acidophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ARS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 291 40% v/v MPD, 0.1M sodium acetate, 0.02M calcium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.57 α = 90 b = 118.57 β = 90 c = 72.92 γ = 120
Symmetry Space Group P 31 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 200 CCD ADSC QUANTUM 315r VORTEX FLUORESCENCE DETECTOR 2009-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 38.81
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 2ARS 2.7 38.81 15063 789 100 0.2 0.198 0.1953 0.254 0.251 RANDOM 51.56
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] -0.03 -0.01 -0.03 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.478 r_dihedral_angle_3_deg 19.139 r_dihedral_angle_4_deg 17.592 r_dihedral_angle_1_deg 6.489 r_scangle_it 3.872 r_scbond_it 2.427 r_mcangle_it 1.742 r_angle_refined_deg 1.547 r_mcbond_it 1.012 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.478 r_dihedral_angle_3_deg 19.139 r_dihedral_angle_4_deg 17.592 r_dihedral_angle_1_deg 6.489 r_scangle_it 3.872 r_scbond_it 2.427 r_mcangle_it 1.742 r_angle_refined_deg 1.547 r_mcbond_it 1.012 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.196 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2761 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 24
Software Software Software Name Purpose ADSC data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling