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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 3.38 63.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 203.84 α = 90 b = 203.84 β = 90 c = 203.84 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 2016-05-19 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 2.2 50 100 0.101 57.5 20.7 36279
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 2.2 2.24 0.468
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XGZ 2.21 30.002 36245 1868 99.893 0.164 0.1623 0.1959 0.1836 RANDOM 30.421
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 23.159 r_dihedral_angle_3_deg 16.577 r_dihedral_angle_6_deg 16.399 r_lrange_other 7.005 r_lrange_it 7.004 r_dihedral_angle_1_deg 6.964 r_scangle_it 5.555 r_scangle_other 5.554 r_mcangle_other 4.276 r_mcangle_it 4.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.159 r_dihedral_angle_3_deg 16.577 r_dihedral_angle_6_deg 16.399 r_lrange_other 7.005 r_lrange_it 7.004 r_dihedral_angle_1_deg 6.964 r_scangle_it 5.555 r_scangle_other 5.554 r_mcangle_other 4.276 r_mcangle_it 4.274 r_scbond_it 3.909 r_scbond_other 3.908 r_mcbond_it 2.95 r_mcbond_other 2.936 r_angle_refined_deg 1.688 r_angle_other_deg 1.12 r_nbd_other 0.384 r_symmetry_nbd_refined 0.342 r_nbd_refined 0.22 r_symmetry_xyhbond_nbd_refined 0.204 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.041 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3602 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing