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Crystasl Structure of Beta-glucosidase D2-BGL from Chaetomella Raphigera
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 10% (w/v) PEG 3000, 0.2 M magnesium chloride, 0.1 M sodium cacodylate, pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.774 α = 90 b = 77.661 β = 90 c = 123.481 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 93 CCD ADSC QUANTUM 210 2013-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.000 SPring-8 BL12B2
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 93.8 0.09 27.7 8 49111
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 91.5 0.475 8.2
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 4IIB 1.9 24.19 46547 2504 93.58 0.14726 0.14473 0.1567 0.19495 0.1998 RANDOM 16.774
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] -1.22 -0.23 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.042 r_dihedral_angle_4_deg 21.561 r_dihedral_angle_3_deg 15.143 r_dihedral_angle_1_deg 6.485 r_long_range_B_refined 4.289 r_long_range_B_other 4.112 r_scangle_other 2.958 r_angle_refined_deg 1.996 r_scbond_it 1.995 r_scbond_other 1.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.042 r_dihedral_angle_4_deg 21.561 r_dihedral_angle_3_deg 15.143 r_dihedral_angle_1_deg 6.485 r_long_range_B_refined 4.289 r_long_range_B_other 4.112 r_scangle_other 2.958 r_angle_refined_deg 1.996 r_scbond_it 1.995 r_scbond_other 1.992 r_mcangle_it 1.987 r_mcangle_other 1.987 r_mcbond_it 1.424 r_mcbond_other 1.411 r_angle_other_deg 1.022 r_chiral_restr 0.173 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 5277 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing