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Beta-1,4-galactanase from Bacteroides thetaiotaomicron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FHL SCWRL4 model was made from 1FHL, 1HJQ, 4BF7,1HJS experimental model PDB 1HJQ SCWRL4 model was made from 1FHL, 1HJQ, 4BF7,1HJS experimental model PDB 4BF7 SCWRL4 model was made from 1FHL, 1HJQ, 4BF7,1HJS experimental model PDB 1HJS SCWRL4 model was made from 1FHL, 1HJQ, 4BF7,1HJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 22% PEG6000, 200 mM NH4Cl, MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.02 39.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.213 α = 90 b = 44.681 β = 99.38 c = 137.546 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 110 IMAGE PLATE MAR scanner 345 mm plate Helios 2015-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.93 46.583 94.8 0.073 0.09 0.053 0.997 14 2.7 40545
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.98 81.1 0.324 0.409 0.247 0.801 2.4
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 SCWRL4 model was made from 1FHL, 1HJQ, 4BF7,1HJS 1.93 46.583 38606 1915 94.29 0.176 0.1735 0.1817 0.2247 0.2295 RANDOM 22.498
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] -0.04 -0.04 0.06 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.716 r_dihedral_angle_4_deg 16.314 r_dihedral_angle_3_deg 13.348 r_dihedral_angle_1_deg 6.86 r_angle_refined_deg 1.356 r_angle_other_deg 0.921 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.716 r_dihedral_angle_4_deg 16.314 r_dihedral_angle_3_deg 13.348 r_dihedral_angle_1_deg 6.86 r_angle_refined_deg 1.356 r_angle_other_deg 0.921 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4939 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction