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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 3.28 62.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.842 α = 90 b = 201.842 β = 90 c = 201.842 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 CCD RAYONIX MX300HE 2016-04-21 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 2.38 50 99.9 0.122 80.3 25.7 28007
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 2.38 2.42 0.68
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 2.39 30 26641 1353 99.81 0.15917 0.15716 0.1662 0.19768 0.2003 RANDOM 35.863
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_2_deg 32.441 r_dihedral_angle_4_deg 16.968 r_dihedral_angle_3_deg 15.781 r_dihedral_angle_1_deg 7.477 r_long_range_B_refined 6.76 r_long_range_B_other 6.757 r_scangle_other 5.352 r_mcangle_it 4.652 r_mcangle_other 4.651 r_scbond_it 3.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.441 r_dihedral_angle_4_deg 16.968 r_dihedral_angle_3_deg 15.781 r_dihedral_angle_1_deg 7.477 r_long_range_B_refined 6.76 r_long_range_B_other 6.757 r_scangle_other 5.352 r_mcangle_it 4.652 r_mcangle_other 4.651 r_scbond_it 3.616 r_scbond_other 3.616 r_mcbond_it 3.084 r_mcbond_other 3.076 r_angle_refined_deg 1.749 r_angle_other_deg 1.364 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 3603 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing