☰ Navigation Tabs
Crystal structure of the sialic acid binding periplasmic protein SiaP
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 36 MG/ML SIAP (IN 20 MM HEPES, 10 MM NACL,AND NEU5GC 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 = 47.73 α = 90 b = 74.49 β = 90 c = 87.48 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 2009-08-13 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 1.37 32.25 100 0.08 12.8 7 62379 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 1.37 1.45 100 0.62 2.5 6.8
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 1.37 32.25 62379 3336 100 0.118 0.116 0.1324 0.158 0.167 2V4C 9.88
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] -0.2 -0.22 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.939 r_dihedral_angle_3_deg 12.18 r_dihedral_angle_4_deg 9.021 r_dihedral_angle_1_deg 5.67 r_scangle_it 5.108 r_scbond_it 3.663 r_mcangle_it 2.419 r_angle_other_deg 2.293 r_angle_refined_deg 1.681 r_mcbond_it 1.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.939 r_dihedral_angle_3_deg 12.18 r_dihedral_angle_4_deg 9.021 r_dihedral_angle_1_deg 5.67 r_scangle_it 5.108 r_scbond_it 3.663 r_mcangle_it 2.419 r_angle_other_deg 2.293 r_angle_refined_deg 1.681 r_mcbond_it 1.668 r_rigid_bond_restr 1.66 r_mcbond_other 1.288 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.002 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 2431 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling