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SiaP in complex with Neu5Gc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V4C PDB ENTRY 2V4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277 30 MG/ML SIAP (IN 20 MM HEPES, 10 MM NACL, PH 8.0) AND EQUAL VOLUME OF RESERVOIR SOLUTION (100MM MES PH 6.0, 28.5% PEG 6K, 3% W/V 1,5-DIAMINOPENTANE DIHYDROCHLORIDE), TEMPERATURE 277K
Crystal Properties Matthews coefficient Solvent content 2.2 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.407 α = 90 b = 74.8 β = 90 c = 87.334 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 2009-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.5 40 98.4 0.11 19.4 8 49622 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 1.5 1.53 96.1 0.56 2.3 4.8
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 2V4C 1.5 40.04 47069 2517 98.4 0.13488 0.13249 0.1418 0.1791 0.1892 RANDOM 13.936
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] -1.2 -0.36 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.579 r_dihedral_angle_3_deg 12.518 r_dihedral_angle_4_deg 9.699 r_dihedral_angle_1_deg 5.644 r_scangle_it 5.38 r_scbond_it 3.893 r_mcangle_it 2.403 r_mcbond_it 1.669 r_angle_refined_deg 1.601 r_rigid_bond_restr 1.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.579 r_dihedral_angle_3_deg 12.518 r_dihedral_angle_4_deg 9.699 r_dihedral_angle_1_deg 5.644 r_scangle_it 5.38 r_scbond_it 3.893 r_mcangle_it 2.403 r_mcbond_it 1.669 r_angle_refined_deg 1.601 r_rigid_bond_restr 1.514 r_angle_other_deg 0.991 r_mcbond_other 0.594 r_chiral_restr 0.106 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2428 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing