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Crystal structure of the human ephrin A2 ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C8X PDB entries 3C8X, 2E7H experimental model PDB 2E7H PDB entries 3C8X, 2E7H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 290.9 3.0% PEG 4000, 0.1M Sodium acetate, 0.1 M Cacodylate pH 5.5, 0.5 M NDSB 256, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K
Crystal Properties Matthews coefficient Solvent content 3.08 60.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.358 α = 90 b = 89.992 β = 90 c = 136.476 γ = 90
Symmetry Space Group P 21 21 2
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 2008-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97948 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 2.5 41 99.7 0.07 22.43 4.1 25966 -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) 1 2.5 2.59 98.1 0.375 2.94 4 2510
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 PDB entries 3C8X, 2E7H 2.5 40.59 24331 1311 98.49 0.24873 0.246 0.2553 0.29943 0.3104 RANDOM 35.468
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] -5.42 9.4 -3.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_4_deg 19.003 r_dihedral_angle_3_deg 17.374 r_dihedral_angle_1_deg 6.639 r_mcangle_it 1.259 r_angle_refined_deg 1.241 r_scangle_it 1.126 r_mcbond_it 0.725 r_scbond_it 0.709 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_4_deg 19.003 r_dihedral_angle_3_deg 17.374 r_dihedral_angle_1_deg 6.639 r_mcangle_it 1.259 r_angle_refined_deg 1.241 r_scangle_it 1.126 r_mcbond_it 0.725 r_scbond_it 0.709 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3658 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling