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Crystal structure of the sialyltransferase CST-II N51A in complex with CMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RO8 PDB ENTRY 1RO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100 MM HEPES5, PH 7.5, 8% (W/V) POLYETHYLENE GLYCOL 6000, 5% (V/V) 2-METHYL-2,4-PENTANEDIOL.
Crystal Properties Matthews coefficient Solvent content 2.48 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.19 α = 90 b = 116.19 β = 90 c = 46.951 γ = 90
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 MIRRORS 2008-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 35 100 0.08 16.6 4.4 21401 3
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 2.11 100 0.41 3.3 4.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RO8 2 35 20305 1098 99.98 0.18788 0.18565 0.1862 0.23005 0.2326 RANDOM 24.557
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] -1.42 -1.42 2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.07 r_dihedral_angle_3_deg 13.101 r_dihedral_angle_1_deg 5.266 r_dihedral_angle_4_deg 3.821 r_scangle_it 2.039 r_scbond_it 1.299 r_angle_refined_deg 0.986 r_mcangle_it 0.75 r_mcbond_it 0.393 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.07 r_dihedral_angle_3_deg 13.101 r_dihedral_angle_1_deg 5.266 r_dihedral_angle_4_deg 3.821 r_scangle_it 2.039 r_scbond_it 1.299 r_angle_refined_deg 0.986 r_mcangle_it 0.75 r_mcbond_it 0.393 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 2147 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing