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Ligand binding domain of EPHA7
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 4.8 291 0.3 M NH4SO4, 0.6 M LiSO4, 0.1 M tri-NaCitrate pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.617 α = 90 b = 140.699 β = 90 c = 143.783 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
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 2.3 20 100 0.057 36.4 6.3 123900 -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) 2.3 2.34 100 0.555 3.9 6.2
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 2.3 19.97 117396 6230 99.75 0.2368 0.23505 0.2285 0.26894 0.2599 RANDOM 45.134
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] 0.64 -0.19 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.343 r_dihedral_angle_3_deg 14.127 r_dihedral_angle_4_deg 12.118 r_dihedral_angle_1_deg 6.052 r_scangle_it 1.33 r_angle_refined_deg 0.967 r_scbond_it 0.792 r_mcangle_it 0.654 r_mcbond_it 0.348 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.343 r_dihedral_angle_3_deg 14.127 r_dihedral_angle_4_deg 12.118 r_dihedral_angle_1_deg 6.052 r_scangle_it 1.33 r_angle_refined_deg 0.967 r_scbond_it 0.792 r_mcangle_it 0.654 r_mcbond_it 0.348 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15203 Nucleic Acid Atoms Solvent Atoms 610 Heterogen Atoms 52
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling