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Crystal structure of beta-ketothiolase BktB B from Ralstonia eutropha H16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 PEG3350, Li2SO4, pH 6.5, vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.954 α = 90 b = 107.236 β = 90 c = 144.137 γ = 90
Symmetry Space Group C 2 2 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 Quantum 270 2013-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97985 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.29 35.74 31979
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 1DLU 2.29 35.74 31979 1570 85.43 0.2654 0.2532 0.2508 0.3189 0.3177 RANDOM 58.836
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] -2.95 2.2 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.618 r_dihedral_angle_3_deg 21.569 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_1_deg 8.2 r_mcangle_it 6.617 r_mcbond_it 4.411 r_mcbond_other 4.411 r_angle_refined_deg 1.732 r_angle_other_deg 0.886 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.618 r_dihedral_angle_3_deg 21.569 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_1_deg 8.2 r_mcangle_it 6.617 r_mcbond_it 4.411 r_mcbond_other 4.411 r_angle_refined_deg 1.732 r_angle_other_deg 0.886 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5718 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling