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Crystal structure of Ruminiclostridium Thermocellum beta-Glucosidase A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291.15 Lithium sulfate monohydrate, BIS-TRIS, Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.28 46.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.67 α = 90 b = 56.22 β = 100.2 c = 94.5 γ = 90
Symmetry Space Group P 1 21 1
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 2009-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97300 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 93.01 94.61 20.7 5 120756
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 1QOX 1.6 93.01 112516 5902 94.61 0.18438 0.18271 0.1927 0.21612 0.2208 RANDOM 19.626
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] 0.6 0.18 -0.06 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.302 r_dihedral_angle_4_deg 19.387 r_dihedral_angle_3_deg 14.139 r_dihedral_angle_1_deg 6.617 r_long_range_B_refined 5.374 r_long_range_B_other 5.374 r_scangle_other 3.963 r_scbond_it 2.648 r_scbond_other 2.648 r_mcangle_it 2.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.302 r_dihedral_angle_4_deg 19.387 r_dihedral_angle_3_deg 14.139 r_dihedral_angle_1_deg 6.617 r_long_range_B_refined 5.374 r_long_range_B_other 5.374 r_scangle_other 3.963 r_scbond_it 2.648 r_scbond_other 2.648 r_mcangle_it 2.547 r_mcangle_other 2.547 r_angle_refined_deg 2.021 r_mcbond_it 1.826 r_mcbond_other 1.826 r_angle_other_deg 1.119 r_chiral_restr 0.133 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 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 7316 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing