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crystal structure of the human EphA4 ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X10 PDB ENTRY 2X10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.8 M AMMONIUM PHOSPHATE, 100 MM HEPES PH 7.4, ADDITIVE = EPHRINB2 IN A 1:1 MOLAR RATIO. WE SAW NO SIGN OF EPHRINB2 IN THE CRYSTAL STRUCTURE. THE USUAL BINDING SITE ON HEPHA4 WAS OCCUPIED BY AN EPHA4-EPHA4 CRYSTAL CONTACT.
Crystal Properties Matthews coefficient Solvent content 6.16 76.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.89 α = 90 b = 166.89 β = 90 c = 192.09 γ = 120
Symmetry Space Group P 32 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 M SINGLE WAVELENGTH 2 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24 2 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.65 83 99.9 0.19 14.7 20 34863 144.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.65 3.7 100 0.48 20
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 ENTRY 2X10 3.65 48.18 34842 1753 99.91 0.3513 0.3495 0.3821 0.3858 0.3849 RANDOM 124.97
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] -7.8639 -7.8639 15.7278
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.35 t_omega_torsion 1.21 t_angle_deg 0.85 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.35 t_omega_torsion 1.21 t_angle_deg 0.85 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd 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 6344 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement xia2 data reduction XDS data reduction xia2 data scaling XSCALE data scaling PHASER phasing