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Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with 1-Kestose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ANN PDB ENTRY 5ANN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 PROTEIN WAS CRYSTALLIZED FROM 1.2M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1M TRIS-HCL PH 8.5, THEN SOAKED IN 30MM 1-KESTOSE
Crystal Properties Matthews coefficient Solvent content 4.08 70.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.526 α = 90 b = 205.019 β = 90 c = 145.988 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M MIRRORS 2014-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9786 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.78 118.92 99.9 0.06 19.5 6.7 213888
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 1.78 1.81 99.8 0.53 3.3 6.8
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 PDB ENTRY 5ANN 1.78 118.92 203088 10689 99.89 0.17109 0.1704 0.18 0.18414 0.1928 RANDOM 26.572
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] 1.49 -2.54 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.501 r_dihedral_angle_4_deg 17.872 r_dihedral_angle_3_deg 10.211 r_dihedral_angle_1_deg 6.755 r_scangle_it 2.669 r_scbond_it 1.637 r_angle_refined_deg 1.402 r_mcangle_it 1.398 r_angle_other_deg 1.091 r_mcbond_it 0.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.501 r_dihedral_angle_4_deg 17.872 r_dihedral_angle_3_deg 10.211 r_dihedral_angle_1_deg 6.755 r_scangle_it 2.669 r_scbond_it 1.637 r_angle_refined_deg 1.402 r_mcangle_it 1.398 r_angle_other_deg 1.091 r_mcbond_it 0.911 r_mcbond_other 0.911 r_chiral_restr 0.103 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9588 Nucleic Acid Atoms Solvent Atoms 1641 Heterogen Atoms 889
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing