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Methanosaeta concilii ATP citrate lyase (D541A mutant) in complex with (3S)-citryl-CoA.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.02 M xylitol
0.02 M myo-inositol
0.02 M D-(-)-fructose
0.02 M L-rhamnose monohydrate
0.02 M D-sorbitol
0.1 M BES/Triethanolamine pH 7.5
12.5 % PEG4000
20 % 1,2,6-hexanetriol
Crystal Properties Matthews coefficient Solvent content 3.36 63.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.531 α = 90 b = 154.373 β = 90 c = 276.054 γ = 90
Symmetry Space Group I 2 2 2
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 EIGER X 16M Toroidal mirror 2020-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976245 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.12 139 99.2 0.0107 0.999 18.58 13.6 88579 44.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.25 96.5 2.596 0.511 0.92 11.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6hxi 2.121 79.04 88580 4490 99.2 0.1866 0.1857 0.2034 0.189 RANDOM 103.91
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] 4.4514 1.7136 -6.165
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.08 t_omega_torsion 2.97 t_angle_deg 0.93 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_utility_distance t_utility_angle
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.08 t_omega_torsion 2.97 t_angle_deg 0.93 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_utility_distance t_utility_angle t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7909 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 79
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing