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STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN COMPLEX WITH 3-b-Galactopyranosyl glucose
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 3-O-beta-D-Galactopyranosyl-D-glucose
Crystal Properties Matthews coefficient Solvent content 2.9 57.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.134 α = 90 b = 111.641 β = 90 c = 125.8 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 100 PIXEL DECTRIS PILATUS3 6M Kbmirrors 2015-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97872 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 2.45 83.5 97.6 0.176 0.981 8.1 6.7 44772
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 2.45 2.54 100 0.528 3.6 6.8
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 5IFP 2.45 83.5 42486 2187 97.47 0.15189 0.14973 0.1581 0.1932 0.1989 RANDOM 21.241
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] 1.53 -0.12 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.347 r_dihedral_angle_4_deg 14.954 r_dihedral_angle_3_deg 12.244 r_dihedral_angle_1_deg 6.659 r_long_range_B_refined 3.43 r_long_range_B_other 3.288 r_scangle_other 1.947 r_mcangle_it 1.456 r_mcangle_other 1.456 r_angle_refined_deg 1.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.347 r_dihedral_angle_4_deg 14.954 r_dihedral_angle_3_deg 12.244 r_dihedral_angle_1_deg 6.659 r_long_range_B_refined 3.43 r_long_range_B_other 3.288 r_scangle_other 1.947 r_mcangle_it 1.456 r_mcangle_other 1.456 r_angle_refined_deg 1.338 r_scbond_it 1.139 r_scbond_other 1.139 r_angle_other_deg 0.954 r_mcbond_it 0.832 r_mcbond_other 0.831 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 604 Heterogen Atoms 352
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing