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Crystal structure of acyl-CoA synthetase from Metallosphaera sedula in complex with Coenzyme A and 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, HANGING DROP 5.2 293 Protein solution(~3 mg/ml) was mixed to a final volume of 1 uL in 1:1 ratio with reservoir solution containing 0.1M acetate pH 5.2, 0.2M NaCl, 6-8% PEG 1500.
Crystal Properties Matthews coefficient Solvent content 2.48 50.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.806 α = 90 b = 93.19 β = 91.12 c = 131.685 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS EIGER2 X 16M 2019-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 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 3.1 52.95 99.9 0.207 0.246 0.132 0.981 4.2 3.4 23358
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 3.1 3.31 99.9 1.132 1.35 0.728 0.735 3.4
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 3B7W 3.1 52.95 22090 1249 99.79 0.21387 0.21032 0.2177 0.27664 0.2224 RANDOM 85.011
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] 3.21 1.21 0.17 -3.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.523 r_long_range_B_refined 12.879 r_long_range_B_other 12.879 r_dihedral_angle_2_deg 11.672 r_scangle_other 8.4 r_dihedral_angle_1_deg 7.839 r_mcangle_it 6.924 r_mcangle_other 6.924 r_scbond_it 5.249 r_scbond_other 5.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.523 r_long_range_B_refined 12.879 r_long_range_B_other 12.879 r_dihedral_angle_2_deg 11.672 r_scangle_other 8.4 r_dihedral_angle_1_deg 7.839 r_mcangle_it 6.924 r_mcangle_other 6.924 r_scbond_it 5.249 r_scbond_other 5.248 r_mcbond_it 4.401 r_mcbond_other 4.4 r_angle_refined_deg 2 r_angle_other_deg 0.645 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 9039 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing