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Crystal structure of the second 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 Poly-alanine model of PDB code 1XED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 298 Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 5% glycerol), Reservoir (0.1 M Citric Acid:NaOH pH 3.5, 25% (w/v) PEG 3350), Cryoprotection (30% Glycerol), Vapor Diffusion, Sitting Drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.388 α = 90 b = 35.365 β = 105.96 c = 73.238 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 CCD ADSC QUANTUM 315r MIRRORS 2013-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0750 NSLS X29A
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 1.65 50 98.6 0.082 18.3 6 30181 30181 21.9
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 1.65 1.68 94 0.702 1.89 5 1467
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Poly-alanine model of PDB code 1XED 1.65 50 30082 1522 98.62 0.181 0.18 0.1887 0.1992 0.2099 RANDOM 27.9053
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] 0.84 -0.77 1.15 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.297 r_dihedral_angle_4_deg 21.406 r_dihedral_angle_3_deg 11.739 r_dihedral_angle_1_deg 6.358 r_mcangle_it 3.486 r_mcbond_it 2.163 r_mcbond_other 2.15 r_angle_refined_deg 1.531 r_angle_other_deg 0.768 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.297 r_dihedral_angle_4_deg 21.406 r_dihedral_angle_3_deg 11.739 r_dihedral_angle_1_deg 6.358 r_mcangle_it 3.486 r_mcbond_it 2.163 r_mcbond_other 2.15 r_angle_refined_deg 1.531 r_angle_other_deg 0.768 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1675 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-3000 data reduction SCALEPACK data scaling PHASER phasing