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Phosphoketolase from Bifidobacterium Breve complexed with inorganic phosphate
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 3.33 63.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.906 α = 90 b = 173.906 β = 90 c = 163.522 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 4r mirrors 2008-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 Photon Factory BL-6A
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 2.3 50 100 0.108 24.9 11.4 55669 55630 28.3
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) 2.3 2.38 100 0.355 4.7 10.4 5490
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 2.3 40.88 55630 52685 2814 99.72 0.17929 0.17676 0.1752 0.22608 0.2249 RANDOM 28.516
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 38.541 r_dihedral_angle_4_deg 20.762 r_dihedral_angle_3_deg 15.852 r_dihedral_angle_1_deg 7.141 r_scangle_it 4.53 r_scbond_it 3.028 r_angle_refined_deg 1.904 r_mcangle_it 1.671 r_mcbond_it 0.964 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.541 r_dihedral_angle_4_deg 20.762 r_dihedral_angle_3_deg 15.852 r_dihedral_angle_1_deg 7.141 r_scangle_it 4.53 r_scbond_it 3.028 r_angle_refined_deg 1.904 r_mcangle_it 1.671 r_mcbond_it 0.964 r_chiral_restr 0.141 r_bond_refined_d 0.023 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 6379 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 50
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing