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beta-fructosidase from Thermotoga maritima in complex with raffinose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UYP PDB ENTRY 1UYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 HANGING DROP TECHNIQUE 10% PEG 1000, 50 MM LI2SO4, 100 MM CITRATE PHOSPHATE BUFFER PH 4.2, CONCENTRATION PROTEIN 8 MG/ML, INCUBATION TEMPERATURE 20 C
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.5 α = 90 b = 114.7 β = 98.9 c = 130 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 294 CCD ADSC CCD MIRRORS 2004-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.87 129.099 97.7 0.062 6 3.3 225700
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 1.87 30 97.8 0.184 3.9 3
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 1UYP 1.87 40 209387 11055 97.7 0.199 0.198 0.2131 0.229 0.2409 RANDOM 15.8
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] 0.91 1.14 -0.64 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.484 r_scangle_it 1.729 r_angle_refined_deg 1.103 r_scbond_it 1.044 r_angle_other_deg 0.854 r_mcangle_it 0.792 r_symmetry_hbond_refined 0.5 r_mcbond_it 0.413 r_symmetry_vdw_refined 0.293 r_nbd_other 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.484 r_scangle_it 1.729 r_angle_refined_deg 1.103 r_scbond_it 1.044 r_angle_other_deg 0.854 r_mcangle_it 0.792 r_symmetry_hbond_refined 0.5 r_mcbond_it 0.413 r_symmetry_vdw_refined 0.293 r_nbd_other 0.233 r_symmetry_vdw_other 0.222 r_nbd_refined 0.183 r_xyhbond_nbd_refined 0.136 r_nbtor_other 0.085 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 21109 Nucleic Acid Atoms Solvent Atoms 1888 Heterogen Atoms 237
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling