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STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN COMPLEX WITH 6-b-Galactopyranosyl galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IFP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 24% (W/V) PEG 3350, 0.1M BIS-TRIS BUFFER PH 6.0 , 0.2M LITHIUM SULPHATE, then soacked in 30mM 6-O-beta-D-Galactopyranosyl-D-galactose, and cryoprotected with 20% (W/V) PEG 400
Crystal Properties Matthews coefficient Solvent content 2.42 49.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.1 α = 90 b = 106.393 β = 99.18 c = 83.723 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 100 PIXEL DECTRIS PILATUS 6M Kbmirrors 2014-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97949 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.27 82.65 99.9 0.157 0.99 8.4 6.8 46487
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 2.27 2.34 99.9 0.584 3.3 6.6
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 5IFP 2.27 82.65 44046 2413 99.91 0.18132 0.17857 0.1875 0.23204 0.2322 RANDOM 23.497
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] 2.48 1.51 -1.57 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.382 r_dihedral_angle_4_deg 16.926 r_dihedral_angle_3_deg 12.635 r_dihedral_angle_1_deg 6.415 r_long_range_B_refined 3.162 r_long_range_B_other 3.136 r_scangle_other 2.198 r_mcangle_other 1.601 r_mcangle_it 1.6 r_scbond_it 1.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.382 r_dihedral_angle_4_deg 16.926 r_dihedral_angle_3_deg 12.635 r_dihedral_angle_1_deg 6.415 r_long_range_B_refined 3.162 r_long_range_B_other 3.136 r_scangle_other 2.198 r_mcangle_other 1.601 r_mcangle_it 1.6 r_scbond_it 1.327 r_scbond_other 1.327 r_angle_refined_deg 1.31 r_mcbond_it 0.946 r_mcbond_other 0.941 r_angle_other_deg 0.746 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 7483 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 406
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing