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Structure of the EphA4 LBD in complex with peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.2M MgCl2, 0.1M Tris pH8.5, 25% PEG3350, 3% 1,6-hexanediol
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.22 α = 90 b = 127.19 β = 90 c = 84.599 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS HTC 2013-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.41 50.83 92.3 0.067 0.041 0.996 13.1 3.6 27979
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.51 80.6 0.226 0.138 0.935 4.8 3.3 2766
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.41 40.14 27951 1439 91.92 0.1767 0.1733 0.2406 0.2603 RANDOM 22.933
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] -20.34 10.53 19.36 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.407 r_dihedral_angle_3_deg 15.804 r_dihedral_angle_4_deg 14.486 r_dihedral_angle_1_deg 7.771 r_mcangle_it 1.709 r_angle_refined_deg 1.419 r_mcbond_other 0.951 r_mcbond_it 0.95 r_angle_other_deg 0.743 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.407 r_dihedral_angle_3_deg 15.804 r_dihedral_angle_4_deg 14.486 r_dihedral_angle_1_deg 7.771 r_mcangle_it 1.709 r_angle_refined_deg 1.419 r_mcbond_other 0.951 r_mcbond_it 0.95 r_angle_other_deg 0.743 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6040 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 140
Software Software Software Name Purpose CrystalClear data collection MOSFLM data reduction Aimless data scaling REFMAC refinement Coot model building PDB_EXTRACT data extraction