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Structure of ATP citrate lyase from Methanothrix soehngenii in complex with citrate and coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other ACL structure from C. limicola
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 14% PEG3350
4% tacsimate pH 8.0
Protein sample buffer:
20 mM citrate pH 6.0, 150 mM NaCl
10 mM CoASH
Crystal Properties Matthews coefficient Solvent content 2.54 51.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.451 α = 90 b = 275.02 β = 90 c = 72.722 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 2M 2017-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00003 SLS X06DA
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 2.1 39.1 99.4 0.112 0.999 13.07 6.1 138565 38.49
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 2.1 2.23 97.1 0.1415 0.387 1.09 5.1
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 ACL structure from C. limicola 2.1 30.75 138531 6962 99.4 0.181 0.179 0.2003 0.208 0.2296 RANDOM 63.6
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] 0.9937 -4.4494 3.4557
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.6 t_omega_torsion 2.97 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.6 t_omega_torsion 2.97 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15704 Nucleic Acid Atoms Solvent Atoms 724 Heterogen Atoms 177
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing