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Crystal structure of succinate-semialdehyde dehydrogenase from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EK1 PDB entry 3EK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 2 mg/mL protein, crystal tracking ID 108914b8, PACT screen B8,
0.1 M MES pH 6.1, 20% PEG 6000, 0.2 M ammonium chloride,
VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.656 α = 90 b = 164.873 β = 92.01 c = 278.901 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 2008-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03317 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 2.7 50 98.6 0.104 10.3 2.9 453409
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 2.7 2.8 98.2 0.692 1.6 2.8 44884
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 PDB entry 3EK1 2.7 49.47 453148 22748 98.29 0.238 0.236 0.2348 0.282 0.2794 RANDOM 40.767
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] 1.36 -0.55 -0.25 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.482 r_dihedral_angle_3_deg 17.802 r_dihedral_angle_4_deg 16.75 r_dihedral_angle_1_deg 5.387 r_scangle_it 1.445 r_angle_refined_deg 1.096 r_scbond_it 0.822 r_mcangle_it 0.535 r_mcbond_it 0.275 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.482 r_dihedral_angle_3_deg 17.802 r_dihedral_angle_4_deg 16.75 r_dihedral_angle_1_deg 5.387 r_scangle_it 1.445 r_angle_refined_deg 1.096 r_scbond_it 0.822 r_mcangle_it 0.535 r_mcbond_it 0.275 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 56733 Nucleic Acid Atoms Solvent Atoms 862 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling