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Crystal structure of rice BGlu1 E176Q/Y341A/Q187A 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, 0.18M ammonium sulfate, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.581 α = 90 b = 101.257 β = 90 c = 127.426 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 105 CCD ADSC QUANTUM 315 2012-12-13 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 1.85 30 97.5 0.077 25.5 7.5 85615
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 1.85 1.92 96.4 0.416 4.9 7.5 8338
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 1.85 27.93 85615 81095 4250 96.85 0.16223 0.16104 0.1714 0.18517 0.1936 RANDOM 17.547
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] -1.29 1.23 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.201 r_dihedral_angle_4_deg 20.772 r_dihedral_angle_3_deg 11.89 r_dihedral_angle_1_deg 5.808 r_long_range_B_refined 4.278 r_long_range_B_other 3.931 r_scangle_other 1.956 r_angle_refined_deg 1.307 r_scbond_it 1.222 r_scbond_other 1.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.201 r_dihedral_angle_4_deg 20.772 r_dihedral_angle_3_deg 11.89 r_dihedral_angle_1_deg 5.808 r_long_range_B_refined 4.278 r_long_range_B_other 3.931 r_scangle_other 1.956 r_angle_refined_deg 1.307 r_scbond_it 1.222 r_scbond_other 1.222 r_mcangle_it 1.124 r_mcangle_other 1.124 r_angle_other_deg 1.015 r_mcbond_it 0.707 r_mcbond_other 0.706 r_chiral_restr 0.122 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7596 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