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Structural basis for specific recognition of reelin by its receptors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E26 PDB ENTRY 2E26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 36-38% MPD, 21-25% PEG 1000, 100mM HEPES-Na pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.98 α = 90 b = 93.844 β = 107.41 c = 73.456 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 CCD Bruker DIP-6040 2006-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.6 46.93 96.6 0.074 0.074 7.5 3.7 21990 -3 56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 97.5 0.374 0.374 1.8 3.5 3213
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 2E26 2.6 46.93 20837 1135 96.45 0.22695 0.22324 0.225 0.29603 0.2956 RANDOM 57.776
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] -3.85 -4.93 -1.77 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.98 r_dihedral_angle_4_deg 16.151 r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 6.875 r_scangle_it 1.459 r_angle_refined_deg 1.229 r_scbond_it 0.927 r_mcangle_it 0.642 r_mcbond_it 0.378 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.98 r_dihedral_angle_4_deg 16.151 r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 6.875 r_scangle_it 1.459 r_angle_refined_deg 1.229 r_scbond_it 0.927 r_mcangle_it 0.642 r_mcbond_it 0.378 r_nbtor_refined 0.308 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.197 r_metal_ion_refined 0.161 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5696 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 76
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling