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Structure of the Leukemia Inhibitory Factor Receptor (LIF-R) domains D1-D5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q7N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 0.1 M Sodium Citrate pH 5.0, 0.1 M Lithium Sulfate, 8% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.42 72.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.008 α = 90 b = 143.169 β = 110.38 c = 80.362 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 140 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
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 3.1 30 98.2 0.098 10.8 3.1 16991 74.762
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 3.1 3.27 98.9 0.611 2 3.2 2480
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.1 30 16071 872 97.86 0.25476 0.25184 0.2633 0.30862 RANDOM 94.338
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] 5.72 6.84 -0.88 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.904 r_dihedral_angle_3_deg 17.911 r_dihedral_angle_4_deg 17.675 r_dihedral_angle_1_deg 3.975 r_scangle_it 1.918 r_mcangle_it 1.899 r_angle_refined_deg 1.363 r_mcbond_it 1.208 r_scbond_it 1.202 r_symmetry_vdw_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.904 r_dihedral_angle_3_deg 17.911 r_dihedral_angle_4_deg 17.675 r_dihedral_angle_1_deg 3.975 r_scangle_it 1.918 r_mcangle_it 1.899 r_angle_refined_deg 1.363 r_mcbond_it 1.208 r_scbond_it 1.202 r_symmetry_vdw_refined 0.335 r_nbtor_refined 0.323 r_nbd_refined 0.29 r_symmetry_hbond_refined 0.261 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3844 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection MOSFLM data reduction SCALA data scaling PHASER phasing