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Crystal structure of the engineered 1,3-1,4-beta-glucanase protein from Bacillus licheniformis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GBG PDB ENTRY 1GBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 16% PEG MME 2000, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.551 α = 61.38 b = 54.813 β = 85.72 c = 54.91 γ = 86.1
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 mirrors 2008-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9795 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 30 93.5 0.043 0.037 18.7 1.8 14740 14739 1 1 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 79.2 0.121 0.126 6.25 1.6 14739
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GBG 2.4 30 1 1 14740 14011 731 93.43 0.21259 0.21042 0.2183 0.25481 0.2706 RANDOM 19.538
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] -1.17 -0.24 -0.16 0.48 0.39 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.258 r_dihedral_angle_4_deg 15.648 r_dihedral_angle_3_deg 11.135 r_dihedral_angle_1_deg 6.291 r_angle_refined_deg 1.093 r_angle_other_deg 1.055 r_scangle_it 0.508 r_mcangle_it 0.436 r_scbond_it 0.325 r_mcbond_it 0.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.258 r_dihedral_angle_4_deg 15.648 r_dihedral_angle_3_deg 11.135 r_dihedral_angle_1_deg 6.291 r_angle_refined_deg 1.093 r_angle_other_deg 1.055 r_scangle_it 0.508 r_mcangle_it 0.436 r_scbond_it 0.325 r_mcbond_it 0.244 r_chiral_restr 0.182 r_nbtor_refined 0.18 r_nbd_other 0.177 r_nbd_refined 0.148 r_xyhbond_nbd_refined 0.133 r_symmetry_vdw_refined 0.133 r_symmetry_vdw_other 0.12 r_nbtor_other 0.079 r_metal_ion_refined 0.072 r_xyhbond_nbd_other 0.033 r_symmetry_hbond_refined 0.031 r_mcbond_other 0.023 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2953 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DNA data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing