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The structure of the GH35 beta-galactosidase Bgl35A from Cellvibrio japonicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U7V PDB ENTRY 3U7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 2.8 M SODIUM ACETATE PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.68 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.911 α = 90.21 b = 115.783 β = 90.25 c = 116.036 γ = 90.38
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.8 50 96.4 0.06 8.7 1.8 459893 -3.7 22.8
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 1.8 1.83 95.1 0.63 1.1 1.8
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 PDB ENTRY 3U7V 1.8 116.03 436784 23101 96.36 0.18617 0.18483 0.1946 0.21153 0.2211 RANDOM 30.008
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] 2 -0.02 0.49 -0.9 0.52 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.547 r_dihedral_angle_4_deg 20.65 r_dihedral_angle_3_deg 13.626 r_dihedral_angle_1_deg 7.064 r_scangle_it 3.852 r_mcangle_it 2.97 r_scbond_it 2.524 r_mcbond_it 2.061 r_mcbond_other 2.061 r_angle_refined_deg 1.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.547 r_dihedral_angle_4_deg 20.65 r_dihedral_angle_3_deg 13.626 r_dihedral_angle_1_deg 7.064 r_scangle_it 3.852 r_mcangle_it 2.97 r_scbond_it 2.524 r_mcbond_it 2.061 r_mcbond_other 2.061 r_angle_refined_deg 1.476 r_angle_other_deg 1.291 r_symmetry_vdw_other 0.305 r_symmetry_vdw_refined 0.29 r_nbd_refined 0.264 r_nbtor_refined 0.184 r_nbd_other 0.183 r_xyhbond_nbd_refined 0.152 r_metal_ion_refined 0.145 r_symmetry_hbond_refined 0.114 r_symmetry_metal_ion_refined 0.112 r_xyhbond_nbd_other 0.106 r_chiral_restr 0.088 r_nbtor_other 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.005 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33480 Nucleic Acid Atoms Solvent Atoms 3581 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing