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Structure of sialic acid binding protein (SiaP) in the presence of KDN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B50 PDB ENTRY 3B50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277 36 MG/ML SIAP (IN 20 MM HEPES, 10 MM NACL, 10 MM KDN, PH 8.0) AND EQUAL VOLUME OF RESERVOIR SOLUTION (100MM MES PH 6.0 28.5% PEG 6K); TEMPERATURE 277K
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.399 α = 90 b = 74.502 β = 90 c = 86.402 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC CCD 2008-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.7 50 99.2 0.09 17.5 6.5 34122
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 1.7 1.73 93.9 0.44 2.43 5.2
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 3B50 1.7 41.56 32329 1711 98.75 0.1457 0.14309 0.1418 0.19397 0.1927 RANDOM 21.302
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] -0.07 0.09 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.142 r_dihedral_angle_3_deg 14.998 r_dihedral_angle_4_deg 9.095 r_dihedral_angle_1_deg 5.427 r_scangle_it 5.153 r_scbond_it 4.268 r_mcangle_it 2.153 r_angle_refined_deg 1.567 r_mcbond_it 1.359 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.142 r_dihedral_angle_3_deg 14.998 r_dihedral_angle_4_deg 9.095 r_dihedral_angle_1_deg 5.427 r_scangle_it 5.153 r_scbond_it 4.268 r_mcangle_it 2.153 r_angle_refined_deg 1.567 r_mcbond_it 1.359 r_chiral_restr 0.115 r_bond_refined_d 0.016 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 2439 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing