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Crystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to fructose 1,6-bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MDB PDB entry 3MDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 BASED ON PACT SCREEN CONDITION F10 WITHOUT NAKHPO4: 100MM BIS-TRIS PROPANE PH 6.5, 20% PEG 3350, 20 MM FRUCTOSE 1,6-BISPHOSPHATE, PROTEIN AT 24.7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 3.32 62.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.46 α = 90 b = 135.82 β = 90 c = 61.54 γ = 90
Symmetry Space Group C 2 2 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 ADSC QUANTUM 315 2010-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.977400 SSRL BL7-1
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 2.37 28.03 99.7 0.081 15.35 4.4 21111 21046 -3 37.35
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 2.37 2.43 99.6 0.479 3.2 4.4 1557
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3MDB 2.37 28.03 20970 1022 0.167 0.165 0.1629 0.208 0.2015 To match 3MBD (random) 24.84
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] -1.28 -0.44 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.606 r_dihedral_angle_4_deg 19.307 r_dihedral_angle_3_deg 15.33 r_dihedral_angle_1_deg 6.078 r_scangle_it 3.871 r_scbond_it 2.35 r_angle_refined_deg 1.499 r_mcangle_it 1.36 r_angle_other_deg 0.9 r_mcbond_it 0.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.606 r_dihedral_angle_4_deg 19.307 r_dihedral_angle_3_deg 15.33 r_dihedral_angle_1_deg 6.078 r_scangle_it 3.871 r_scbond_it 2.35 r_angle_refined_deg 1.499 r_mcangle_it 1.36 r_angle_other_deg 0.9 r_mcbond_it 0.711 r_mcbond_other 0.169 r_chiral_restr 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2617 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 19
Software Software Software Name Purpose Blu-Ice data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing