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Monomer structure of hyperthermophilic beta-glucosidase mutant forming a dodecameric structure in the crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293 0.1M HEPES-NaOH pH7.6, 0.2M Ca-Acetate, 20% PEG 3350, 5% Ethyleneglycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.365 α = 120.08 b = 148.872 β = 94 c = 148.563 γ = 99.7
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 RAYONIX MX-225 2013-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 2.81 48.28 0.11 28.7 170856
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 3WDP 2.81 48.28 156940 8298 96.44 0.2446 0.24299 0.2411 0.27497 0.2725 RANDOM 61.032
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] -2.38 -0.43 0.01 0.59 0.3 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.664 r_dihedral_angle_3_deg 16.414 r_dihedral_angle_4_deg 15.752 r_dihedral_angle_1_deg 6.106 r_angle_refined_deg 1.48 r_angle_other_deg 1.444 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.664 r_dihedral_angle_3_deg 16.414 r_dihedral_angle_4_deg 15.752 r_dihedral_angle_1_deg 6.106 r_angle_refined_deg 1.48 r_angle_other_deg 1.444 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.009 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 43636 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling