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Crystal structure of BvGH123 with bound GalNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L7R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M BisTRis pH 6.0-7.0
17 % PEG MME2k
10 mM GalNAc
Crystal Properties Matthews coefficient Solvent content 2.3 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.345 α = 90 b = 142.207 β = 90 c = 145.806 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 100 PIXEL DECTRIS PILATUS3 6M 2016-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9184 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 65 100 0.104 0.999 12 6.5 68163
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 2.1 2.15 100 1.53 1.2 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5l7r 2.1 64 68085 3283 99.91 0.1943 0.1927 0.2267 0.2047 RANDOM 52.2065
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] -2.67 1.08 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.897 r_dihedral_angle_3_deg 16.537 r_dihedral_angle_4_deg 15.698 r_dihedral_angle_1_deg 6.866 r_angle_other_deg 3.661 r_mcangle_it 2.18 r_angle_refined_deg 1.592 r_mcbond_it 1.369 r_mcbond_other 1.369 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.897 r_dihedral_angle_3_deg 16.537 r_dihedral_angle_4_deg 15.698 r_dihedral_angle_1_deg 6.866 r_angle_other_deg 3.661 r_mcangle_it 2.18 r_angle_refined_deg 1.592 r_mcbond_it 1.369 r_mcbond_other 1.369 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_other 0.013 r_gen_planes_refined 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9016 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing