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SAM Domain of Human Ephrin Type-A Receptor 1 (EphA1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QKQ PDB ENTRY 2QKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.1 22% PEG 3350, 0.3 M
MG(NO4)2. PRIOR TO SETTING UP CRYSTALLIZATION PLATES, CHYMOTRYPSIN WAS ADDED TO THE PROTEIN SAMPLE AT A FINAL CONCENTRATION OF 0.57 MICROMOLAR., pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.1K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.286 α = 90 b = 52.286 β = 90 c = 81.307 γ = 120
Symmetry Space Group P 31 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 270 2009-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.91700 CHESS F1
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 30 100 0.081 43 10.5 9138 9138 -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 2.03 100 0.84 3.64 10.4 447
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 (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 2QKQ 2 30 8696 437 99.99 0.21163 0.21163 0.20829 0.2307 0.27942 0.2905 RANDOM 49.149
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] 0.18 0.09 0.18 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.988 r_dihedral_angle_4_deg 25.019 r_dihedral_angle_3_deg 15.215 r_dihedral_angle_1_deg 5.281 r_scangle_it 3.477 r_scbond_it 2.271 r_angle_refined_deg 1.393 r_mcangle_it 1.264 r_mcbond_it 0.694 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.988 r_dihedral_angle_4_deg 25.019 r_dihedral_angle_3_deg 15.215 r_dihedral_angle_1_deg 5.281 r_scangle_it 3.477 r_scbond_it 2.271 r_angle_refined_deg 1.393 r_mcangle_it 1.264 r_mcbond_it 0.694 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1026 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 5
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling