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Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme EXO1 in complex with PEG400
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IEQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 75mM HEPES-NaOH pH7.0 buffer, 1.2% PEG 400, 1.7M ammonium sulphate
, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.51 64.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.268 α = 90 b = 100.268 β = 90 c = 181.695 γ = 90
Symmetry Space Group P 43 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 CCD ADSC QUANTUM 315 collimating mirror, double-crystal Si(111) monochromator 2006-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 87.71 99.2 81336 81336 1
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 1.8 1.85 97.4 0.99 1.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1IEQ 1.8 48.33 81336 81336 4285 99.22 0.16205 0.16054 0.16 0.19051 0.1892 RANDOM 30.342
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] 0.33 0.33 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.296 r_dihedral_angle_4_deg 16.656 r_dihedral_angle_3_deg 13.283 r_dihedral_angle_1_deg 5.924 r_scangle_it 2.568 r_scbond_it 1.654 r_angle_refined_deg 1.253 r_mcangle_it 0.883 r_mcbond_it 0.555 r_symmetry_hbond_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.296 r_dihedral_angle_4_deg 16.656 r_dihedral_angle_3_deg 13.283 r_dihedral_angle_1_deg 5.924 r_scangle_it 2.568 r_scbond_it 1.654 r_angle_refined_deg 1.253 r_mcangle_it 0.883 r_mcbond_it 0.555 r_symmetry_hbond_refined 0.305 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 4566 Nucleic Acid Atoms Solvent Atoms 883 Heterogen Atoms 248
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling