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Structure of beta glucosidase 1A from Thermotoga neapolitana, mutant E349A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 288 Protein at 12 mg/ml in 20 mM citrate phosphate buffer, pH 5.6. Hanging drops consisting of 1 microlitre of protein solution and 2 microlitres of reservoir solution (18-23% w/v PEG 6000, 0.2 M sodium chloride, 0.1 M sodium acetate, pH 5.0) equilibrated against 1 ml of reservoir solution. Rod-shaped crystals of approximate dimensions 0.3 x 0.2 x 0.3 mm grew after 8-10 days.
Crystal Properties Matthews coefficient Solvent content 2.47 50.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.277 α = 90 b = 98.726 β = 90 c = 154.756 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 MARRESEARCH 2011-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.0402 MAX II I911-2
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 30.1 99.1 0.084 12.6 5 81717
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 1.93 85.4 1.172 1.9
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 2CBV 1.9 30 77455 4096 98.85 0.17082 0.16857 0.1786 0.2147 0.2234 RANDOM 27.434
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] 1.04 -0.42 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.831 r_dihedral_angle_4_deg 21.985 r_dihedral_angle_3_deg 14.176 r_dihedral_angle_1_deg 6.696 r_long_range_B_refined 4.992 r_long_range_B_other 4.947 r_scangle_other 3.433 r_angle_refined_deg 2.24 r_scbond_it 2.202 r_scbond_other 2.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.831 r_dihedral_angle_4_deg 21.985 r_dihedral_angle_3_deg 14.176 r_dihedral_angle_1_deg 6.696 r_long_range_B_refined 4.992 r_long_range_B_other 4.947 r_scangle_other 3.433 r_angle_refined_deg 2.24 r_scbond_it 2.202 r_scbond_other 2.202 r_mcangle_it 1.84 r_mcangle_other 1.84 r_mcbond_it 1.313 r_mcbond_other 1.283 r_angle_other_deg 1.191 r_chiral_restr 0.155 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 7300 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing