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Structure of the citryl-CoA lyase core module of Chlorobium limicola ATP citrate lyase (space group P3121)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other C. limicola ACL holoenzyme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 1.6 M Lithium sulphate
0.1 M Tris pH 8.0
Protein Sample buffer:
20 mM HEPES pH 7.4, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.63 53.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.029 α = 90 b = 110.029 β = 90 c = 92.749 γ = 120
Symmetry Space Group P 31 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 EIGER X 9M 2018-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980042 SOLEIL PROXIMA 2
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 1.7 50 99.9 0.167 0.999 14.87 15.3 71556 3 3 25.82
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 1.7 1.8 99.5 1.542 0.648 1.64 15.4
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 C. limicola ACL holoenzyme 1.7 34 71480 2004 100 0.173 0.173 0.1744 0.192 0.1994 RANDOM 21.96
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] -1.7752 -1.7752 3.5504
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.53 t_omega_torsion 3.45 t_angle_deg 0.92 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 15.53 t_omega_torsion 3.45 t_angle_deg 0.92 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 3960 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 59
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing