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Structure of protein Ta0514, putative lipoate protein ligase from T. acidophilum with bound lipoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C7I PDB ENTRY 2C7I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293 pH 6.70
Crystal Properties Matthews coefficient Solvent content 2.95 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.377 α = 90 b = 117.882 β = 93.51 c = 105.663 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 53.3 99.2 0.064 20 4 97539 2
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 2 2.08 99.2 0.21 5.4 4
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 PDB ENTRY 2C7I 1.89 53.3 97539 5132 99.2 0.208 0.207 0.2237 0.239 0.2519 RANDOM 32.53
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] -0.02 -0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.95 r_dihedral_angle_4_deg 19.594 r_dihedral_angle_3_deg 12.716 r_scangle_it 5.942 r_dihedral_angle_1_deg 5.316 r_scbond_it 4.464 r_mcangle_it 2.619 r_mcbond_it 1.993 r_angle_refined_deg 1.095 r_symmetry_hbond_refined 0.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.95 r_dihedral_angle_4_deg 19.594 r_dihedral_angle_3_deg 12.716 r_scangle_it 5.942 r_dihedral_angle_1_deg 5.316 r_scbond_it 4.464 r_mcangle_it 2.619 r_mcbond_it 1.993 r_angle_refined_deg 1.095 r_symmetry_hbond_refined 0.535 r_xyhbond_nbd_refined 0.475 r_nbtor_refined 0.317 r_nbd_refined 0.267 r_symmetry_vdw_refined 0.221 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7510 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing