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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 3.34 63.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 203.051 α = 90 b = 203.051 β = 90 c = 203.051 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 2017-10-12 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 1.81 50 100 0.086 77.5 33.6 64454
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 1.81 1.84 0.824
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XGZ 1.812 30.002 64441 3209 99.95 0.159 0.1581 0.1702 0.1848 0.1936 RANDOM 18.54
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_6_deg 16.434 r_dihedral_angle_2_deg 15.195 r_dihedral_angle_3_deg 15.052 r_lrange_it 6.995 r_lrange_other 6.995 r_dihedral_angle_1_deg 6.483 r_scangle_it 5.475 r_scangle_other 5.474 r_scbond_it 3.53 r_scbond_other 3.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.434 r_dihedral_angle_2_deg 15.195 r_dihedral_angle_3_deg 15.052 r_lrange_it 6.995 r_lrange_other 6.995 r_dihedral_angle_1_deg 6.483 r_scangle_it 5.475 r_scangle_other 5.474 r_scbond_it 3.53 r_scbond_other 3.529 r_mcangle_it 3.231 r_mcangle_other 3.231 r_mcbond_it 2.159 r_mcbond_other 2.159 r_angle_refined_deg 1.718 r_angle_other_deg 0.998 r_nbd_other 0.251 r_nbd_refined 0.228 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.19 r_symmetry_nbd_refined 0.189 r_xyhbond_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_other 0.141 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.08 r_bond_other_d 0.037 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3598 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing