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Crystallographic analysis of the polysialic acid O-acetyltransferase OatWY
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other IN-HOUSE STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 100 MM SODIUM ACETATE, 2.25 M AMMONIUM ACETATE, pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.63 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.669 α = 90 b = 94.393 β = 90 c = 100.874 γ = 90
Symmetry Space Group P 2 2 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 MARMOSAIC 225 mm CCD MIRRORS 2008-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-1
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 1.9 40 99 0.05 52.8 10 59306 7
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 1.9 1.97 95.2 0.28 7.2 8.9
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 IN-HOUSE STRUCTURE 1.9 40 56022 2987 98.48 0.19473 0.19278 0.2261 0.23106 0.2544 RANDOM 16.569
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] 3.35 -1.24 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.984 r_dihedral_angle_3_deg 13.409 r_dihedral_angle_4_deg 12.046 r_dihedral_angle_1_deg 6.133 r_scangle_it 2.99 r_scbond_it 1.884 r_angle_refined_deg 1.342 r_angle_other_deg 1.044 r_mcangle_it 0.987 r_mcbond_it 0.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.984 r_dihedral_angle_3_deg 13.409 r_dihedral_angle_4_deg 12.046 r_dihedral_angle_1_deg 6.133 r_scangle_it 2.99 r_scbond_it 1.884 r_angle_refined_deg 1.342 r_angle_other_deg 1.044 r_mcangle_it 0.987 r_mcbond_it 0.513 r_mcbond_other 0.16 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_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 4856 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement HKL data reduction SCALEPACK data scaling PHASER phasing