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Ex vivo Ym2 crystal structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 310 Single ex vivo Ym2 crystals were harvested from the BAL fluid of transgenic C57BL/6J-Tg(CAG-Gal10)Bla mice and cryoprotected by a brief soak in PBS + 35% (v/v) glycerol.
Crystal Properties Matthews coefficient Solvent content 2.06 40.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.261 α = 90 b = 60.205 β = 94.24 c = 60.173 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2018-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000089224 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.7 60.01 97.7 0.177 0.992 6.59 3.47 39074 24.584
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.81 1.364 0.358 0.96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.71 16.78 39026 2014 97.8 0.178 0.177 0.1819 0.205 0.2101 RANDOM 19.24
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] -2.5256 -1.3217 -1.2762 3.8018
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.6 t_omega_torsion 3.57 t_angle_deg 0.97 t_bond_d 0.01 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_other_torsion 15.6 t_omega_torsion 3.57 t_angle_deg 0.97 t_bond_d 0.01 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 2970 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 6
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing