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Crystal structure of glycopeptide 22 in complex with scFv-SM3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A2I PDB ENTRY 5A2I
Crystallization Crystal Properties Matthews coefficient Solvent content 2.06 40.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.349 α = 90 b = 67.875 β = 90 c = 90.889 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 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
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 2.05 20 98.5 0.12 10.4 7.8 14126 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 2.05 2.16 92.2 0.78 2.1 5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5A2I 2.05 54.38 13637 406 97.94 0.20171 0.19979 0.27672 0.26 RANDOM 37.924
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] -0.29 3.4 -3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.843 r_dihedral_angle_4_deg 18.322 r_dihedral_angle_3_deg 15.555 r_dihedral_angle_1_deg 6.813 r_mcangle_it 2.968 r_scbond_it 2.156 r_mcbond_it 1.864 r_mcbond_other 1.86 r_angle_refined_deg 1.397 r_angle_other_deg 0.748
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.843 r_dihedral_angle_4_deg 18.322 r_dihedral_angle_3_deg 15.555 r_dihedral_angle_1_deg 6.813 r_mcangle_it 2.968 r_scbond_it 2.156 r_mcbond_it 1.864 r_mcbond_other 1.86 r_angle_refined_deg 1.397 r_angle_other_deg 0.748 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_it 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 1757 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling MOLREP phasing