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Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other CCL core module from C. limicola
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Na2SO4 pH 6.7
20% PEG3350
Protein sample buffer:
20 mM HEPES pH 7.4
150 mM NaCl
supplemented with 50 mM Citrate pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.29 46.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.341 α = 90 b = 123.89 β = 90 c = 139.796 γ = 90
Symmetry Space Group P 21 21 21
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 2018-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9762 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 1.85 67.34 99.8 0.205 0.996 8.69 9.2 100132 25.12
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 1.85 1.96 99.5 1.606 0.499 8.7 9.2
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 CCL core module from C. limicola 1.85 61.94 100130 4982 99.7 0.166 0.165 0.1678 0.193 0.1953 RANDOM 29.67
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] 2.9164 -0.1965 -2.72
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.73 t_omega_torsion 3.5 t_angle_deg 1.01 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 14.73 t_omega_torsion 3.5 t_angle_deg 1.01 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 8104 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 107
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing