☰ Navigation Tabs
Citryl-CoA lyase core module of Chlorobium limicola ATP citrate lyase in complex with acetyl-CoA and L-malate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.1 293 0.2 M Calcium chloride
20% PEG 3350 pH 5.1
Protein buffer:
20 mM HEPES, pH 7.4
150 mM NaCl
10 mM acetyl-CoA
50 mM L-Malate
Crystal Properties Matthews coefficient Solvent content 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.73 α = 90 b = 100.817 β = 102.99 c = 105.012 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2018-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.6 45.62 98.8 0.126 0.998 11.86 6.8 270869 20.51
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 1.6 1.7 97.6 0.1462 0.552 1.31 6.9
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 6hxj 1.6 45.62 270868 13820 98.8 0.158 0.157 0.1594 0.177 0.1816 RANDOM 27.7
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] -3.1731 -0.5593 2.1299 1.0432
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.36 t_omega_torsion 3.87 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 14.36 t_omega_torsion 3.87 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 15543 Nucleic Acid Atoms Solvent Atoms 1066 Heterogen Atoms 288
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing