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1.65A crystal structure of isocitrate dehydrogenase from Burkholderia pseudomallei
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 289 20% PEG 3350, 2M POTASSIUM FORMATE, pH 7, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.14 42.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.993 α = 90 b = 62.238 β = 118.52 c = 70.998 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 300 mm CCD ADJUSTABLE FOCUSING MIRRORS 2008-04-04 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.00 APS 23-ID-D
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 1.65 45.68 99.8 0.043 13.9 3.35 47920
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 1.65 1.71 99.3 0.286 2.9 2.79 4720
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.65 45.69 47920 2427 99.82 0.206 0.205 0.203 0.234 0.2294 RANDOM 23.227
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] 0.12 -0.07 -0.04 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.799 r_dihedral_angle_4_deg 13.271 r_dihedral_angle_3_deg 12.559 r_dihedral_angle_1_deg 5.468 r_scangle_it 2.072 r_scbond_it 1.292 r_angle_refined_deg 1.013 r_mcangle_it 0.804 r_mcbond_it 0.515 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.799 r_dihedral_angle_4_deg 13.271 r_dihedral_angle_3_deg 12.559 r_dihedral_angle_1_deg 5.468 r_scangle_it 2.072 r_scbond_it 1.292 r_angle_refined_deg 1.013 r_mcangle_it 0.804 r_mcbond_it 0.515 r_nbtor_refined 0.301 r_nbd_refined 0.179 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.106 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3211 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling