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Structure of the H13A mutant of Ykr043C in complex with fructose-1,6-bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F3K PDB entry 3F3K molecule A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 resevoir of 0.1M Sodium Hepes ph7.5, 10% isopropanol and 20% PEG4K. 0.03 mg/ml trypsin was added to the protein prior to crystallization setup. Crystals were washed in well solution, then soaked in well solution plus 12% Glycerol and 0.1M fructose 1,6 bis-phosphate at room temperature for 10 minutes prior to flash-freezing in liquid N2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.67 53.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.62 α = 90 b = 84.022 β = 90 c = 101.568 γ = 90
Symmetry Space Group P 21 21 21
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 2009-12-14 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) R Sym 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 31.39 98 0.104 0.104 21.28 5 25683 25181 -3 40.9
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 2.5 2.54 89.1 0.484 4.7 4.9 1215
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 3F3K molecule A 2.49 31.39 25160 23890 1270 97.63 0.22468 0.22254 0.2209 0.2663 0.2641 RANDOM 28.3
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] -0.01 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.353 r_dihedral_angle_3_deg 16.567 r_dihedral_angle_4_deg 15.494 r_dihedral_angle_1_deg 6.175 r_scangle_it 2.884 r_scbond_it 1.837 r_angle_refined_deg 1.554 r_mcangle_it 1.137 r_mcbond_it 0.651 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.353 r_dihedral_angle_3_deg 16.567 r_dihedral_angle_4_deg 15.494 r_dihedral_angle_1_deg 6.175 r_scangle_it 2.884 r_scbond_it 1.837 r_angle_refined_deg 1.554 r_mcangle_it 1.137 r_mcbond_it 0.651 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.306 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4208 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 40
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling