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Structure of the EphA4 LBD in complex with peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WO1
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, 4% 1,3-butanediol
Crystal Properties Matthews coefficient Solvent content 2.25 45.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.27 α = 90 b = 127.69 β = 90 c = 84.569 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 2012-03-26 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 2.42 50.95 93.4 0.083 0.034 0.995 14.4 6.6 27280
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 2.42 2.52 90.1 0.246 0.104 0.971 4.9 6.3 2882
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 2WO1 2.42 50.95 27253 1346 92.99 0.1735 0.1706 0.1745 0.2325 0.2257 RANDOM 43.273
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] -4.62 16.89 27.25 -22.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.641 r_dihedral_angle_3_deg 16.947 r_dihedral_angle_4_deg 12.899 r_dihedral_angle_1_deg 7.796 r_mcangle_it 1.645 r_angle_refined_deg 1.468 r_mcbond_it 0.921 r_mcbond_other 0.921 r_angle_other_deg 0.734 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.641 r_dihedral_angle_3_deg 16.947 r_dihedral_angle_4_deg 12.899 r_dihedral_angle_1_deg 7.796 r_mcangle_it 1.645 r_angle_refined_deg 1.468 r_mcbond_it 0.921 r_mcbond_other 0.921 r_angle_other_deg 0.734 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6090 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 60
Software Software Software Name Purpose CrystalClear data collection MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction