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Crystal structure of rice BGlu1 E176Q/Y341A mutant complexed with cellotetraose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 288 20% PEG MME 5000, 0.2M ammonium sulfate, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.34 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.66 α = 90 b = 79.531 β = 97.83 c = 101.989 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 105 CCD ADSC QUANTUM 315 2012-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.83 30 98.7 0.084 13.7 3.4 87554
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.9 92.8 0.465 2 2.2 8189
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 Rigid body refinement THROUGHOUT 3F5I 1.83 30 87554 75154 3951 88.94 0.15281 0.15198 0.1613 0.16854 0.1785 RANDOM 19.1
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] 0.12 0.09 -0.11 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.141 r_dihedral_angle_4_deg 21.097 r_dihedral_angle_3_deg 11.872 r_dihedral_angle_1_deg 5.733 r_long_range_B_refined 4.404 r_long_range_B_other 4.114 r_scangle_other 1.938 r_angle_refined_deg 1.28 r_scbond_it 1.227 r_scbond_other 1.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.141 r_dihedral_angle_4_deg 21.097 r_dihedral_angle_3_deg 11.872 r_dihedral_angle_1_deg 5.733 r_long_range_B_refined 4.404 r_long_range_B_other 4.114 r_scangle_other 1.938 r_angle_refined_deg 1.28 r_scbond_it 1.227 r_scbond_other 1.227 r_mcangle_it 1.059 r_mcangle_other 1.059 r_angle_other_deg 1.058 r_mcbond_it 0.67 r_mcbond_other 0.666 r_chiral_restr 0.114 r_bond_refined_d 0.008 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7604 Nucleic Acid Atoms Solvent Atoms 839 Heterogen Atoms 170
Software Software Software Name Purpose HKL-2000 data collection Coot model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling