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Crystal structure of isocitrate lyase from Brucella melitensis, bound to magnesium isocitrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 290 Internal tracking number 217292B10. Protein (26 mg/mL) and PACT Screen condition B10: 0.2 M MgCl2, 20% PEG6000, 0.1 M MES pH 6.0, 5 mM isocitrate, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.91 α = 90 b = 135.93 β = 90 c = 181.79 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+ 2010-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2.35 47.6 99.8 0.101 12.13 3.8 80134 79958 -3 28.906
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 2.35 2.41 99.2 0.563 2 2.9 5866
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3OQ8 2.35 47.6 80134 79682 3991 99.46 0.18 0.18 0.178 0.1803 0.23 0.2294 RANDOM 22.264
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] 1.12 -0.38 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.778 r_dihedral_angle_4_deg 17.585 r_dihedral_angle_3_deg 14.061 r_dihedral_angle_1_deg 5.671 r_scangle_it 2.34 r_scbond_it 1.417 r_angle_refined_deg 1.246 r_angle_other_deg 0.879 r_mcangle_it 0.818 r_mcbond_it 0.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.778 r_dihedral_angle_4_deg 17.585 r_dihedral_angle_3_deg 14.061 r_dihedral_angle_1_deg 5.671 r_scangle_it 2.34 r_scbond_it 1.417 r_angle_refined_deg 1.246 r_angle_other_deg 0.879 r_mcangle_it 0.818 r_mcbond_it 0.431 r_mcbond_other 0.113 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12879 Nucleic Acid Atoms Solvent Atoms 687 Heterogen Atoms 80
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction