☰ Navigation Tabs
Phosphoketolase from Bifidobacterium Breve complexed with dihydroxyethyl 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 3.32 62.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.529 α = 90 b = 173.529 β = 90 c = 163.516 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 210 mirrors 2010-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 42.8 14.9 72417 72387 22.2
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 0.298 11 15 3587
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3AHC 2.1 49.07 72387 68524 3637 99.73 0.16294 0.16066 0.20639 0.1755 RANDOM 22.304
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 38.121 r_dihedral_angle_4_deg 19.398 r_dihedral_angle_3_deg 14.018 r_dihedral_angle_1_deg 6.918 r_scangle_it 4.743 r_scbond_it 3.328 r_angle_refined_deg 2.066 r_mcangle_it 1.916 r_mcbond_it 1.19 r_chiral_restr 0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.121 r_dihedral_angle_4_deg 19.398 r_dihedral_angle_3_deg 14.018 r_dihedral_angle_1_deg 6.918 r_scangle_it 4.743 r_scbond_it 3.328 r_angle_refined_deg 2.066 r_mcangle_it 1.916 r_mcbond_it 1.19 r_chiral_restr 0.166 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 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 797 Heterogen Atoms 104
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing