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Structure of Giardia fructose-1,6-biphosphate aldolase in complex with 3-hydroxy-2-pyridone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 18-25% Polyethylglycol 3350, 0.2 M NH4NO3, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0 K
Crystal Properties Matthews coefficient Solvent content 2.11 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.58 α = 90 b = 64.95 β = 90 c = 171.45 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 CCD MARMOSAIC 225 mm CCD mirrors 2008-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 20 86.6 0.079 25998 22497
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 89.1 0.248
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3GAY 2.3 20 22497 1204 86.6 0.20259 0.19878 0.1975 0.27388 0.2685 RANDOM 30.772
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 37.366 r_dihedral_angle_4_deg 22.928 r_dihedral_angle_3_deg 17.764 r_dihedral_angle_1_deg 6.197 r_mcangle_it 4.1 r_scangle_it 3.998 r_mcbond_it 3.832 r_scbond_it 3.214 r_angle_refined_deg 1.534 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.366 r_dihedral_angle_4_deg 22.928 r_dihedral_angle_3_deg 17.764 r_dihedral_angle_1_deg 6.197 r_mcangle_it 4.1 r_scangle_it 3.998 r_mcbond_it 3.832 r_scbond_it 3.214 r_angle_refined_deg 1.534 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.222 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.097 r_bond_refined_d 0.014 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4857 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 42
Software Software Software Name Purpose PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling