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Crystal structure of acyl-COA synthetase from Metallosphaera sedula in complex with acetyl-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B7W 3B7W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 293 Drops of 3 mg/ml protein solution dispensed with a Mosquito robot into MRC-SD2 plates containing commercial screens with different ratios (1.25:0.75, 0.75:1.25).
Best crystals grown in 0.1M acetic acid pH 5.2, 200mM NaCl, 7-10% PEG3350. Crystals appeared after 24h.
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.864 α = 90 b = 88.289 β = 92.97 c = 131.207 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 PIXEL DECTRIS EIGER2 X 16M 2019-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.8 66.48 99.7 0.165 0.234 0.165 0.962 3.2 1.9 56843
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.88 99.9 0.817 1.156 0.817 0.527 1.8
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 3B7W 2.8 66.48 54003 2810 99.68 0.23648 0.23456 0.2382 0.27325 0.2469 RANDOM 60.627
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] 1.37 -0.47 -1.28 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.468 r_dihedral_angle_2_deg 14.22 r_dihedral_angle_1_deg 7.708 r_long_range_B_refined 5.865 r_long_range_B_other 5.865 r_scangle_other 2.919 r_mcangle_it 2.457 r_mcangle_other 2.456 r_angle_refined_deg 2.048 r_scbond_it 1.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.468 r_dihedral_angle_2_deg 14.22 r_dihedral_angle_1_deg 7.708 r_long_range_B_refined 5.865 r_long_range_B_other 5.865 r_scangle_other 2.919 r_mcangle_it 2.457 r_mcangle_other 2.456 r_angle_refined_deg 2.048 r_scbond_it 1.733 r_scbond_other 1.733 r_mcbond_it 1.481 r_mcbond_other 1.481 r_angle_other_deg 0.659 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18032 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing