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Crystal Structure of domain VI and LE1 of human Netrin-G2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 20% PEG 3350, 0.2M Calcium acetate, 0.1M Sodium cacodylate pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.81 56.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.134 α = 90 b = 63.134 β = 90 c = 190.64 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 CCD ADSC QUANTUM 4 2011-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 1.071 NSLS X4A
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 1.8 30 5.6 40558 1 1
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 1.8 1.86 74.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 SAD THROUGHOUT 1.8 28.27 1 40558 38026 2020 95.9 0.178 0.175 0.1847 0.227 0.2383 RANDOM 29.44
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] 0.83 0.41 0.83 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.289 r_dihedral_angle_4_deg 18.592 r_dihedral_angle_3_deg 14.662 r_dihedral_angle_1_deg 7.163 r_scangle_it 5.774 r_scbond_it 3.752 r_mcangle_it 2.571 r_angle_refined_deg 2.272 r_mcbond_it 1.578 r_chiral_restr 0.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.289 r_dihedral_angle_4_deg 18.592 r_dihedral_angle_3_deg 14.662 r_dihedral_angle_1_deg 7.163 r_scangle_it 5.774 r_scbond_it 3.752 r_mcangle_it 2.571 r_angle_refined_deg 2.272 r_mcbond_it 1.578 r_chiral_restr 0.184 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 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 2662 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 69
Software Software Software Name Purpose HKL-2000 data collection SHELXS phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling