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Structure of the SAM Domain of Human Ephrin Type-B Receptor 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 298 2.3 M NaKPO4, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.92 35.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.566 α = 90 b = 73.566 β = 90 c = 25.679 γ = 90
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 300 mm CCD mirrors 2007-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97918 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 37 98.6 0.064 39 7.3 8210 8210 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 95.5 0.73 2.87 7.2 772
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1F0M 2.1 36.79 7859 7859 349 98.67 0.22071 0.21952 0.2195 0.24406 0.2389 RANDOM 39.737
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] 1.25 1.25 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.574 r_dihedral_angle_4_deg 19.48 r_dihedral_angle_3_deg 17.196 r_dihedral_angle_1_deg 4.041 r_scangle_it 1.389 r_angle_refined_deg 1.006 r_scbond_it 0.984 r_mcangle_it 0.525 r_mcbond_it 0.32 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.574 r_dihedral_angle_4_deg 19.48 r_dihedral_angle_3_deg 17.196 r_dihedral_angle_1_deg 4.041 r_scangle_it 1.389 r_angle_refined_deg 1.006 r_scbond_it 0.984 r_mcangle_it 0.525 r_mcbond_it 0.32 r_nbtor_refined 0.301 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.155 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 948 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing