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Crystal structure of isocitrate lyase from Brucella melitensis, bound to the product mimic malonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EOL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 Internal tracking number 217291H3. Hampton INDEX Screen condition H3: 0.2 M sodium malonate pH 7.0, 20% PEG3350, BrabA.00014.a.A1 PW 25251 at 26 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.54 51.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.5 α = 90 b = 136.03 β = 90 c = 181.77 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 CCD RIGAKU SATURN 944+ 2010-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.541780
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 39.2 99.3 0.14 10.38 4.8 91893 91241 -3 24.311
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.31 99.2 0.479 4.2 4.6 6734
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3EOL 2.25 39.2 91893 90916 4530 98.97 0.151 0.151 0.149 0.199 0.1638 RANDOM 16.324
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] 0.56 0.47 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_4_deg 18.468 r_dihedral_angle_3_deg 13.625 r_dihedral_angle_1_deg 6.013 r_scangle_it 3.426 r_scbond_it 2.145 r_angle_refined_deg 1.494 r_mcangle_it 1.108 r_angle_other_deg 0.951 r_mcbond_it 0.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_4_deg 18.468 r_dihedral_angle_3_deg 13.625 r_dihedral_angle_1_deg 6.013 r_scangle_it 3.426 r_scbond_it 2.145 r_angle_refined_deg 1.494 r_mcangle_it 1.108 r_angle_other_deg 0.951 r_mcbond_it 0.604 r_mcbond_other 0.204 r_chiral_restr 0.088 r_bond_refined_d 0.017 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 12903 Nucleic Acid Atoms Solvent Atoms 1177 Heterogen Atoms 81
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction