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Crystal structure of the 1st Ig domain from mouse Polymeric Immunoglobulin receptor [PSI-NYSGRC-006220]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 5% glycerol), Reservoir (0.2M MgCl2, 0.1M Bis-Tris-HCl, 25% (v/v) PEG 3350), Cryoprotection (33% Ethylene glycol), Vapor Diffusion, Sitting Drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.275 α = 90 b = 46.803 β = 90 c = 62.062 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 MIRRORS 2013-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0750 NSLS X25
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 1.51 50 99.4 0.077 8.1 11.9 18980
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 1.51 1.54 93.3 0.353 8 853
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 1XED 1.51 37.37 18374 945 96.48 0.1625 0.161 0.1891 0.2273 RANDOM 17.001
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] -0.24 -0.32 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.652 r_dihedral_angle_4_deg 16.227 r_dihedral_angle_3_deg 12.295 r_dihedral_angle_1_deg 5.685 r_mcangle_it 3.184 r_angle_refined_deg 2.214 r_mcbond_it 1.933 r_mcbond_other 1.93 r_angle_other_deg 0.947 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.652 r_dihedral_angle_4_deg 16.227 r_dihedral_angle_3_deg 12.295 r_dihedral_angle_1_deg 5.685 r_mcangle_it 3.184 r_angle_refined_deg 2.214 r_mcbond_it 1.933 r_mcbond_other 1.93 r_angle_other_deg 0.947 r_chiral_restr 0.138 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 858 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 27
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-3000 data reduction MOLREP phasing