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Structure of Neisseria LOS-specific sialyltransferase (NST).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YK5 PDB ENTRY 2YK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.4 PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION METHODS USING DROPS OF PROTEIN MIXED WITH AN EQUAL VOLUME OF PRECIPITANT: 100 MM SODIUM ACETATE (PH 4.2 - 4.4) 1.7 M DI-AMMONIUM SULFATE.
Crystal Properties Matthews coefficient Solvent content 2.97 58.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.565 α = 90 b = 124.735 β = 90 c = 41.866 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 1.94 71.07 100 0.01 35.5 8.8 34365 2
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 1.94 1.97 99.9 0.05 3.22 8.5
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 PDB ENTRY 2YK5 1.94 71.07 32604 1735 99.92 0.19639 0.19499 0.1965 0.22274 0.2227 RANDOM 32.485
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] -1.39 0.23 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.987 r_dihedral_angle_4_deg 18.939 r_dihedral_angle_3_deg 16.014 r_dihedral_angle_1_deg 7.56 r_scangle_it 3.953 r_scbond_it 2.576 r_mcangle_it 1.82 r_angle_refined_deg 1.619 r_mcbond_it 1.036 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.987 r_dihedral_angle_4_deg 18.939 r_dihedral_angle_3_deg 16.014 r_dihedral_angle_1_deg 7.56 r_scangle_it 3.953 r_scbond_it 2.576 r_mcangle_it 1.82 r_angle_refined_deg 1.619 r_mcbond_it 1.036 r_chiral_restr 0.106 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2642 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing