☰ Navigation Tabs
Crystal structure of a prokaryotic beta-1,3-1,4-glucanase (lichenase) derived from a mouse hindgut metagenome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BYH PDB ENTRY 1BYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 0.1M SPG buffer pH 8.0, 25% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.51 51.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.367 α = 90 b = 79.804 β = 90 c = 85.47 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 113 IMAGE PLATE RIGAKU RAXIS IV++ 2009-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.89 37.67 100 0.06 18.6 7 43509 3
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) 1.9 2 100 0.515 3.8 6.9 42997
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1BYH 1.89 37.67 1 56889 41198 2248 98.28 0.1711 0.17267 0.17032 0.1615 0.21549 0.1582 RANDOM 29.048
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] 8.82 -1.51 -7.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.069 r_dihedral_angle_4_deg 19.628 r_dihedral_angle_3_deg 16.249 r_dihedral_angle_1_deg 8.605 r_scangle_it 4.611 r_scbond_it 3.575 r_mcangle_it 2.32 r_mcbond_it 1.585 r_angle_refined_deg 1.473 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.069 r_dihedral_angle_4_deg 19.628 r_dihedral_angle_3_deg 16.249 r_dihedral_angle_1_deg 8.605 r_scangle_it 4.611 r_scbond_it 3.575 r_mcangle_it 2.32 r_mcbond_it 1.585 r_angle_refined_deg 1.473 r_chiral_restr 0.143 r_gen_planes_refined 0.017 r_bond_refined_d 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3487 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling