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Crystal structure of the human ephrin A2 LBD and CRD domains in complex with ephrin A1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C8X PDB ENTRIES 3C8X, 1SHW experimental model PDB 1SHW PDB ENTRIES 3C8X, 1SHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 290.9 10.0% PEG 3350, 0.16M AMMONIUM PHOSPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K
Crystal Properties Matthews coefficient Solvent content 2.91 57.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.265 α = 90 b = 215.787 β = 90 c = 107.263 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 ADSC QUANTUM 315 2008-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.8 39 99.7 0.066 23.65 5.3 16953 -3 83.52
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) 2.8 2.85 100 0.668 2.17 5.3
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 PDB ENTRIES 3C8X, 1SHW 2.81 34.1 16953 16891 874 0.2286 0.2261 0.2379 0.2723 0.2871 RANDOM 80.12
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] 5.0869 -2.0623 -3.0246
RMS Deviations Key Refinement Restraint Deviation t_angle_deg 1.15 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_omega_torsion
RMS Deviations Key Refinement Restraint Deviation t_angle_deg 1.15 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_omega_torsion t_other_torsion t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3207 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 50
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing BUSTER refinement HKL-2000 data reduction HKL-2000 data scaling