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Crystal structure of isocitrate lyase (Caur_3889) from Chloroflexus aurantiacus in complex with isocitrate and manganese ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 35% MPD, 0.1M sodium acetate/acetic acid pH4.5
Crystal Properties Matthews coefficient Solvent content 3.66 66.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.314 α = 90 b = 157.314 β = 90 c = 197.707 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2018-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.9 50 95.9 0.112 0.135 0.074 8 2.9 115739
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 91.7 0.301 0.376 0.221 0.812 2.4
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 3E5B 2.9 32.05 110130 5601 95.9 0.179 0.1756 0.1819 0.2464 0.2471 RANDOM 36.915
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] 0.86 0.43 0.86 -2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.433 r_dihedral_angle_4_deg 18.541 r_dihedral_angle_3_deg 18.064 r_dihedral_angle_1_deg 7.711 r_angle_refined_deg 1.689 r_angle_other_deg 1.337 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.433 r_dihedral_angle_4_deg 18.541 r_dihedral_angle_3_deg 18.064 r_dihedral_angle_1_deg 7.711 r_angle_refined_deg 1.689 r_angle_other_deg 1.337 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26328 Nucleic Acid Atoms Solvent Atoms 683 Heterogen Atoms 184
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing