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A Ykr043C/ fructose-1,6-bisphosphate product complex following ligand soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F3K 3F3K molecule A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.1M tri-Lithium Citrate, 15%PEG3350, 8%MPD with 0.03 mg/ml trypsin in the protein. Soak with 0.1M tri-Lithium Citrate, 15%PEG3350, 8%MPD and 100 mM Fructose-1,6-bisphosphate for 2 hours, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.302 α = 90 b = 83.385 β = 104.19 c = 104.685 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 IMAGE PLATE RIGAKU RAXIS IV++ Mirrors 2009-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 2.5 50 91.3 0.093 12 3 48678 44466 -3 -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) 2.5 2.59 93.3 0.482 2.9 2.7
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 3F3K molecule A 2.6 43.35 39186 37178 2008 91.17 0.22258 0.22003 0.2419 0.2698 0.2895 RANDOM 25.978
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] 0.06 0.02 -0.08 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.535 r_dihedral_angle_3_deg 18.846 r_dihedral_angle_4_deg 17 r_dihedral_angle_1_deg 6.293 r_angle_refined_deg 1.653 r_nbtor_refined 0.32 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.535 r_dihedral_angle_3_deg 18.846 r_dihedral_angle_4_deg 17 r_dihedral_angle_1_deg 6.293 r_angle_refined_deg 1.653 r_nbtor_refined 0.32 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.108 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8688 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 40
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling