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Rice Os3BGlu6 E178Q with Covalent Glucosyl Moiety from p-nitrophenyl glucopyranoside.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNO PDB ENTRY 3GNO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 13% PEG5000MME, 0.1M Bis/Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.61 52.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.986 α = 90 b = 91.127 β = 90 c = 111.221 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 100 CCD ADSC QUANTUM 315 toroidal focusing mirror 2011-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 25.67 97.84 0.06 28.9 6.5 46100 45797 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 1.9 1.97 100 0.41 4.5 6.3
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 PDB ENTRY 3GNO 1.9 25.67 43994 43044 2307 97.84 0.14781 0.14617 0.147 0.17872 0.1804 RANDOM 18.847
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.224 r_dihedral_angle_4_deg 17.045 r_dihedral_angle_3_deg 12.848 r_dihedral_angle_1_deg 6.127 r_scangle_it 3.14 r_scbond_it 1.971 r_mcangle_it 1.31 r_angle_refined_deg 1.282 r_mcbond_it 0.695 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.224 r_dihedral_angle_4_deg 17.045 r_dihedral_angle_3_deg 12.848 r_dihedral_angle_1_deg 6.127 r_scangle_it 3.14 r_scbond_it 1.971 r_mcangle_it 1.31 r_angle_refined_deg 1.282 r_mcbond_it 0.695 r_chiral_restr 0.093 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 3842 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing