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Crystal Structure of Rice BGlu1 E386S Mutant Complexed with alpha-Glucosyl Fluoride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RGL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 288 20% PEG MME 5000, 0.22M ammonium sulfate, 0.1M MES, 0.010M alpha-glucosyl fluoride, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.128 α = 90 b = 100.86 β = 90 c = 127.004 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 2009-08-20 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 99.9 0.122 16.2 7.2 87779
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 99.9 0.437 4.6 7.2 8689
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2RGL 1.85 25.3 83372 4328 99.88 0.17533 0.17382 0.1748 0.20453 0.2056 RANDOM 10.701
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] -0.27 0.89 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.038 r_dihedral_angle_4_deg 20.713 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_1_deg 5.908 r_scangle_it 3.119 r_scbond_it 1.914 r_angle_refined_deg 1.382 r_mcangle_it 1.108 r_mcbond_it 0.586 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.038 r_dihedral_angle_4_deg 20.713 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_1_deg 5.908 r_scangle_it 3.119 r_scbond_it 1.914 r_angle_refined_deg 1.382 r_mcangle_it 1.108 r_mcbond_it 0.586 r_chiral_restr 0.156 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 7612 Nucleic Acid Atoms Solvent Atoms 870 Heterogen Atoms 71
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing