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Crystal Structure of Streptomyces avermitilis beta-L-Arabinopyranosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UAS PDB ENTRY 1UAS, 1XYF experimental model PDB 1XYF PDB ENTRY 1UAS, 1XYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 1.7M ammonium sulfate, 1.7% PEG 400, 15% glycerol, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.205 α = 90 b = 98.916 β = 90 c = 181.265 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 2008-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.983 Photon Factory BL-17A
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 1.5 50 98.1 0.086 30.6 7.8 191711
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 1.5 1.55 91.2 0.335 6.5 8.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1UAS, 1XYF 1.51 33.37 181993 9648 98.89 0.15792 0.15678 0.17946 0.185 RANDOM 13.457
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 36.054 r_dihedral_angle_3_deg 11.012 r_dihedral_angle_4_deg 9.1 r_dihedral_angle_1_deg 6.335 r_scangle_it 1.836 r_scbond_it 1.183 r_angle_refined_deg 1.066 r_mcangle_it 0.742 r_mcbond_it 0.407 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.054 r_dihedral_angle_3_deg 11.012 r_dihedral_angle_4_deg 9.1 r_dihedral_angle_1_deg 6.335 r_scangle_it 1.836 r_scbond_it 1.183 r_angle_refined_deg 1.066 r_mcangle_it 0.742 r_mcbond_it 0.407 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 9032 Nucleic Acid Atoms Solvent Atoms 1827 Heterogen Atoms 269
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing