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Structure of Neisseria LOS-specific sialyltransferase (NST), in complex with CMP-3F-Neu5Ac.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YK4 PDB ENTRY 2YK4
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: 180MM TRI-SODIUM CITRATE, 5 MM MNCL2, 20%(V/V) PEG 1500, PH 6.25 .
Crystal Properties Matthews coefficient Solvent content 2.44 49.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.762 α = 90 b = 101.413 β = 90 c = 166.57 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE MAR scanner 345 mm plate 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
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 2.18 83.33 97.1 0.01 23.9 7.6 19377 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 2.18 2.22 84.9 0.05 2.64 5.4
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 2YK4 2.18 83.33 17844 957 96.95 0.20103 0.19806 0.1946 0.25786 0.2508 RANDOM 29.876
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] -0.88 1.1 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.084 r_dihedral_angle_4_deg 18.324 r_dihedral_angle_3_deg 16.665 r_dihedral_angle_1_deg 5.977 r_scangle_it 3.4 r_scbond_it 2.425 r_angle_refined_deg 1.765 r_mcangle_it 1.563 r_mcbond_it 0.908 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.084 r_dihedral_angle_4_deg 18.324 r_dihedral_angle_3_deg 16.665 r_dihedral_angle_1_deg 5.977 r_scangle_it 3.4 r_scbond_it 2.425 r_angle_refined_deg 1.765 r_mcangle_it 1.563 r_mcbond_it 0.908 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 2612 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing