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The extracellular region of CD33 with bound sialoside analogue P22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 0.1M citrate/phosphate, 6.5% PEG 400, 6.5% PEG 500 MME, 6.5% PEG 600, 6.5% PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.18 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.641 α = 90 b = 103.23 β = 110.42 c = 84.495 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 EIGER2 X 16M 2019-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 79.19 95.5 0.143 0.155 0.06 0.998 10.3 12.8 33360
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 69.9 1.795 2.047 0.954 0.497 1 8.2
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 THROUGHOUT 5IHB 1.95 79.19 31641 1705 95.41 0.1962 0.1936 0.246 0.2325 RANDOM 33.442
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] 0.06 -0.99 -0.08 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.156 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_3_deg 15.01 r_dihedral_angle_1_deg 7.467 r_angle_refined_deg 1.588 r_angle_other_deg 1.243 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.156 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_3_deg 15.01 r_dihedral_angle_1_deg 7.467 r_angle_refined_deg 1.588 r_angle_other_deg 1.243 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3357 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 275
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing