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Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZ4 pdb entry 3ez4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 ButhA.00112.a.A1 PW33325 at 38.6 mg/mL against PACT H2 0.2 M sodium bromide, 0.1 M Bis Tris propane pH 8.5, 20% PEG 3350, crystal tracking ID 225054h2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.71 α = 90 b = 174.75 β = 108.71 c = 104.58 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 CCD ADSC QUANTUM 315r 2011-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 1.8 50 99.9 0.07 23.86 7.4 256134 255864 -3 22.655
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 1.8 1.85 99.8 0.452 4.31 7.1 18885
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 (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 3ez4 1.8 50 256134 255850 12850 99.86 0.155 0.1537 0.1532 0.1801 0.1781 RANDOM 18.1463
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] -1.88 0.49 2.19 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.163 r_dihedral_angle_4_deg 20.491 r_dihedral_angle_3_deg 13.004 r_dihedral_angle_1_deg 5.953 r_angle_refined_deg 1.326 r_angle_other_deg 0.904 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.163 r_dihedral_angle_4_deg 20.491 r_dihedral_angle_3_deg 13.004 r_dihedral_angle_1_deg 5.953 r_angle_refined_deg 1.326 r_angle_other_deg 0.904 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18653 Nucleic Acid Atoms Solvent Atoms 2458 Heterogen Atoms 45
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction