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E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic ligand NV355
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M CaCl2, 0.1 M Mops pH 6.2, 11-14% PEG8000, after microseeding
Crystal Properties Matthews coefficient Solvent content 2.85 56.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.52 α = 90 b = 73.08 β = 94.19 c = 52.45 γ = 90
Symmetry Space Group C 1 2 1
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-F 2016-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.21 46.63 96.4 0.055 0.999 14.9 6.4 17093 64.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.29 81 1.03 0.601 1 4.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4C16 2.21 46.63 17093 855 96.4 0.23 0.229 0.245 0.2579 RANDOM 84
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] -16.4927 -1.7153 -2.342 18.8347
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.41 t_other_torsion 2.97 t_angle_deg 1.13 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.41 t_other_torsion 2.97 t_angle_deg 1.13 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2176 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 144
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing