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H320A mutant of Phosphoketolase from Bifidobacterium Breve complexed with acetyl thiamine diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AHC PDB ENTRY 3AHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 24%(v/v) PEG 6000, 0.1M BICINE buffer, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.36 63.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.426 α = 90 b = 174.426 β = 90 c = 163.809 γ = 90
Symmetry Space Group I 4 2 2
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 mirrors 2009-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.1 50 100 0.071 47.5 14.7 73346 73304 25
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) 2.1 2.14 100 0.305 10.1 14.7 3607
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 3AHC 2.1 34.21 73304 69576 3692 99.96 0.15226 0.1501 0.1491 0.19388 0.1927 RANDOM 25.037
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.85 r_dihedral_angle_4_deg 19.098 r_dihedral_angle_3_deg 13.524 r_dihedral_angle_1_deg 6.712 r_scangle_it 5.247 r_scbond_it 3.515 r_mcangle_it 2.043 r_angle_refined_deg 2.031 r_mcbond_it 1.252 r_chiral_restr 0.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.85 r_dihedral_angle_4_deg 19.098 r_dihedral_angle_3_deg 13.524 r_dihedral_angle_1_deg 6.712 r_scangle_it 5.247 r_scbond_it 3.515 r_mcangle_it 2.043 r_angle_refined_deg 2.031 r_mcbond_it 1.252 r_chiral_restr 0.167 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 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 6374 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 71
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing