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Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-1,5-L-arabinofuranotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AKF PDB ENTRY 3AKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.8M sodium citrate, 0.2M sodium chloride, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.237 α = 90 b = 91.341 β = 90 c = 135.962 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 95 CCD ADSC QUANTUM 270 2007-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.97000 Photon Factory BL-17A
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 1.7 39.47 97.9 0.055 0.055 53.7 14.6 56484 -3 22.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 97 0.257 0.257 9.53 14.4 5492
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 3AKF 1.7 39.47 53483 2877 98 0.18963 0.18799 0.187 0.21972 0.2171 RANDOM 22.698
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] -0.05 0.22 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.278 r_dihedral_angle_4_deg 15.57 r_dihedral_angle_3_deg 11.879 r_dihedral_angle_1_deg 5.878 r_scangle_it 2.774 r_scbond_it 1.727 r_angle_refined_deg 1.244 r_mcangle_it 1.189 r_mcbond_it 0.657 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.278 r_dihedral_angle_4_deg 15.57 r_dihedral_angle_3_deg 11.879 r_dihedral_angle_1_deg 5.878 r_scangle_it 2.774 r_scbond_it 1.727 r_angle_refined_deg 1.244 r_mcangle_it 1.189 r_mcbond_it 0.657 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3518 Nucleic Acid Atoms Solvent Atoms 578 Heterogen Atoms 81
Software Software Software Name Purpose SERGUI data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling