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Crystal Structure of Bifidobacterium Longum Phosphoketolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other the roughly refined crystal structure of the selenomethionine substituted protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 6.6 299 PEG3350, MES, Sodium thiocyanate, pH 6.6, hanging drop, temperature 299K
Crystal Properties Matthews coefficient Solvent content 2.74 55.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.26 α = 90 b = 184.41 β = 97.31 c = 157.44 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 270 2009-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.000 Photon Factory BL-17A
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 2.2 156.16 98.9 0.085 401973 -3 28.555
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 2.2 2.3 93.4 0.29 4.6
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 the roughly refined crystal structure of the selenomethionine substituted protein 2.2 47.87 381743 20230 98.88 0.14981 0.14687 0.1487 0.20552 0.2067 RANDOM 24.12
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] -0.17 -2.4 -1.48 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.188 r_dihedral_angle_4_deg 17.854 r_dihedral_angle_3_deg 15.56 r_dihedral_angle_1_deg 6.926 r_scangle_it 4.865 r_scbond_it 3.208 r_angle_refined_deg 1.933 r_mcangle_it 1.825 r_mcbond_it 1.055 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.188 r_dihedral_angle_4_deg 17.854 r_dihedral_angle_3_deg 15.56 r_dihedral_angle_1_deg 6.926 r_scangle_it 4.865 r_scbond_it 3.208 r_angle_refined_deg 1.933 r_mcangle_it 1.825 r_mcbond_it 1.055 r_chiral_restr 0.136 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 51680 Nucleic Acid Atoms Solvent Atoms 5056 Heterogen Atoms 216
Software Software Software Name Purpose XSCALE data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction