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Alpha-galactosidase mutant D387A from Thermotoga maritima in complex with intact cyclohexene-based carbasugar mimic of galactose with 2,4-dinitro leaving group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M MgSO4, 20% (w/v) poly(ethylene glycol) (PEG) 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.389 α = 90 b = 95.789 β = 90 c = 97.453 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 80 PIXEL DECTRIS PILATUS 6M 2017-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.72 67.32 99.8 0.145 0.106 0.997 9.5 5 67554
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.76 99.5 2.147 2.615 0.552 2.5 4.9
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 5M0X 1.72 55.49 63960 3487 99.48 0.16643 0.16452 0.1764 0.20256 0.2116 RANDOM 21.495
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] 2.44 -0.96 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.448 r_dihedral_angle_4_deg 15.191 r_dihedral_angle_3_deg 13.193 r_dihedral_angle_1_deg 7.198 r_long_range_B_refined 5.963 r_long_range_B_other 5.962 r_scangle_other 4.5 r_scbond_it 2.894 r_scbond_other 2.894 r_mcangle_other 2.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.448 r_dihedral_angle_4_deg 15.191 r_dihedral_angle_3_deg 13.193 r_dihedral_angle_1_deg 7.198 r_long_range_B_refined 5.963 r_long_range_B_other 5.962 r_scangle_other 4.5 r_scbond_it 2.894 r_scbond_other 2.894 r_mcangle_other 2.497 r_mcangle_it 2.492 r_mcbond_it 1.695 r_mcbond_other 1.676 r_angle_refined_deg 1.305 r_angle_other_deg 0.939 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 4307 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing