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Crystal structure of Leukemia inhibitory factor in complex with LIF receptor (domains 1-5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PVH PDB ENTRY 1PVH CHAIN B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 1.5M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 7.866101 84.363281
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.476 α = 90 b = 240.131 β = 90 c = 202.631 γ = 90
Symmetry Space Group C 2 2 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 CCD MARMOSAIC 225 mm CCD mirrors 2005-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.968 APS 22-ID
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 4 20 94.2 0.226 6.3 6.6 37104 37104
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 4 4.14 72.5 0.857 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1PVH CHAIN B 4 20 0.857 35239 35239 1852 93.63 0.23978 0.23978 0.23724 0.2323 0.28696 0.2819 RANDOM 102.084
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] 10.49 -2.61 -7.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.188 r_dihedral_angle_3_deg 24.328 r_dihedral_angle_4_deg 20.222 r_dihedral_angle_1_deg 8.334 r_scangle_it 1.77 r_angle_refined_deg 1.739 r_scbond_it 1.02 r_mcangle_it 0.964 r_mcbond_it 0.527 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.188 r_dihedral_angle_3_deg 24.328 r_dihedral_angle_4_deg 20.222 r_dihedral_angle_1_deg 8.334 r_scangle_it 1.77 r_angle_refined_deg 1.739 r_scbond_it 1.02 r_mcangle_it 0.964 r_mcbond_it 0.527 r_nbtor_refined 0.327 r_nbd_refined 0.279 r_symmetry_vdw_refined 0.235 r_xyhbond_nbd_refined 0.204 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 10252 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 587
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing