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Structure of Neisseria LOS-specific sialyltransferase (NST), in complex with CDP.
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 2.96 58.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.099 α = 90 b = 123.51 β = 90 c = 41.652 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 IMAGE PLATE MARRESEARCH X-RAY MIRRORS OSMIC VARIMAXHR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.83 70.71 99.7 0.121 15.4 6.8 11162 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 2.83 2.88 97.8 0.522 2.7 5.1
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 2.83 70.71 10631 532 99.55 0.19294 0.18985 0.18 0.25654 0.2388 RANDOM 27.571
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] 0.53 -0.51 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.883 r_dihedral_angle_4_deg 22.437 r_dihedral_angle_3_deg 19.14 r_dihedral_angle_1_deg 6.771 r_scangle_it 3.337 r_scbond_it 1.953 r_angle_refined_deg 1.694 r_mcangle_it 1.456 r_mcbond_it 0.756 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.883 r_dihedral_angle_4_deg 22.437 r_dihedral_angle_3_deg 19.14 r_dihedral_angle_1_deg 6.771 r_scangle_it 3.337 r_scbond_it 1.953 r_angle_refined_deg 1.694 r_mcangle_it 1.456 r_mcbond_it 0.756 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 2637 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing