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Crystal structure of the lectin domain of PapG from E. coli BI47 in complex with SSEA4 in space group P212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.15M ZnAcetate, 0.05M ZnCl2, 0.1MTris pH 7.5, 13% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.03 39.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.21 α = 90 b = 52.22 β = 90 c = 76.32 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 PIXEL DECTRIS PILATUS 2M 2013-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00004 SLS X06DA
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 1.8 43.1 99.9 0.081 19.3 8.5 17523
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 1.8 1.91 99.5 0.68 3.5 12.8
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 1j8s 1.8 43.1 17523 923 99.91 0.1804 0.17807 0.191 0.22402 0.2317 RANDOM 28.14
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] -0.44 -0.25 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.814 r_dihedral_angle_4_deg 17.978 r_dihedral_angle_3_deg 14.154 r_dihedral_angle_1_deg 8.109 r_long_range_B_refined 5.481 r_long_range_B_other 5.083 r_scangle_other 3.013 r_mcangle_it 2.46 r_mcangle_other 2.459 r_angle_refined_deg 2.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.814 r_dihedral_angle_4_deg 17.978 r_dihedral_angle_3_deg 14.154 r_dihedral_angle_1_deg 8.109 r_long_range_B_refined 5.481 r_long_range_B_other 5.083 r_scangle_other 3.013 r_mcangle_it 2.46 r_mcangle_other 2.459 r_angle_refined_deg 2.365 r_scbond_it 1.937 r_scbond_other 1.937 r_mcbond_it 1.609 r_mcbond_other 1.604 r_angle_other_deg 1.124 r_chiral_restr 0.132 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1667 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing