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Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme EXO1 in complex with 4-deoxy-glucose
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 3.53 65.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.564 α = 90 b = 100.564 β = 90 c = 181.758 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 MARRESEARCH RH COATED SI MIRROR 2005-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.12714 APS 14-ID-B
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 88.05 99.5 88188 88188 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 1.86 99 0.99 1.3
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 1IEQ 1.8 88.05 82188 4338 99.48 0.15137 0.15015 0.1742 0.1863 RANDOM 29.961
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] 0.49 0.49 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.025 r_dihedral_angle_4_deg 14.096 r_dihedral_angle_3_deg 11.724 r_dihedral_angle_1_deg 6.023 r_scangle_it 2.875 r_scbond_it 1.851 r_angle_refined_deg 1.327 r_mcangle_it 0.986 r_mcbond_it 0.633 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.025 r_dihedral_angle_4_deg 14.096 r_dihedral_angle_3_deg 11.724 r_dihedral_angle_1_deg 6.023 r_scangle_it 2.875 r_scbond_it 1.851 r_angle_refined_deg 1.327 r_mcangle_it 0.986 r_mcbond_it 0.633 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 880 Heterogen Atoms 214
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling