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The crystal structure of the ligand-binding domain of the EphB2 receptor at 2.0 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUK PDB entry 1NUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 295 1.2 M Na/K phosphate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.68 54.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.028 α = 90 b = 54.028 β = 90 c = 157.412 γ = 90
Symmetry Space Group P 41 21 2
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 210 2006-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.97950 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 37.13 15984
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 1NUK 2 37.11 15163 806 96.31 0.20134 0.19833 0.1951 0.2632 0.258 RANDOM 42.247
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] 1.2 1.2 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.82 r_dihedral_angle_4_deg 17.839 r_dihedral_angle_3_deg 17.222 r_dihedral_angle_1_deg 7.148 r_scangle_it 5.568 r_scbond_it 3.477 r_mcangle_it 2.71 r_angle_refined_deg 2.085 r_mcbond_it 1.539 r_chiral_restr 0.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.82 r_dihedral_angle_4_deg 17.839 r_dihedral_angle_3_deg 17.222 r_dihedral_angle_1_deg 7.148 r_scangle_it 5.568 r_scbond_it 3.477 r_mcangle_it 2.71 r_angle_refined_deg 2.085 r_mcbond_it 1.539 r_chiral_restr 0.176 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 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 1503 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling