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Crystal structures of MeBglD2 in complex with various saccharides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Tris-HCl buffer (pH 8.5), 1.2 M lithium sulfate, 0.01 M nickel chloride
Crystal Properties Matthews coefficient Solvent content 3.32 62.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.488 α = 90 b = 202.488 β = 90 c = 202.488 γ = 90
Symmetry Space Group I 4 3 2
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 EIGER X 16M 2015-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 99.9 0.063 25.6 13 61903
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 0.637
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 5XGZ 1.8 30 61901 3241 99.95 0.16186 0.15934 0.1729 0.21005 0.1727 RANDOM 24.276
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.292 r_rigid_bond_restr 7.741 r_dihedral_angle_1_deg 6.768 r_scangle_other 6.5 r_long_range_B_refined 5.928 r_long_range_B_other 5.893 r_scbond_other 5.864 r_scbond_it 5.863 r_mcangle_other 3.958 r_mcangle_it 3.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.292 r_rigid_bond_restr 7.741 r_dihedral_angle_1_deg 6.768 r_scangle_other 6.5 r_long_range_B_refined 5.928 r_long_range_B_other 5.893 r_scbond_other 5.864 r_scbond_it 5.863 r_mcangle_other 3.958 r_mcangle_it 3.956 r_dihedral_angle_2_deg 3.743 r_mcbond_it 3.452 r_mcbond_other 3.452 r_angle_refined_deg 1.774 r_angle_other_deg 0.744 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_bond_other_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3644 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing