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THE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH A FRAGMENT OF DRAXIN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4URT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 298 1.6 M AMMONIUM SULPHATE AND 0.1 M
SODIUM CITRATE, AT PH 4 TO PH 5, VAPOR DIFFUSION, TEMPERATURE
298K
Crystal Properties Matthews coefficient Solvent content 4.62 73.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.794 α = 90 b = 130.794 β = 90 c = 183.87 γ = 120
Symmetry Space Group P 64 2 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 PIXEL DECTRIS PILATUS3 6M 2015-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.987 PETRA III, EMBL c/o DESY P14 (MX2)
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 3.07 54.13 99.9 0.587 8.7 32.9 18063
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.07 3.23 99.7 2.897 18.6
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 4URT 3.07 54.01 17128 874 99.8 0.237 0.235 0.2422 0.271 0.2695 RANDOM 76.42
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] 2.42 1.21 2.42 -7.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.405 r_dihedral_angle_3_deg 18.113 r_dihedral_angle_4_deg 17.203 r_long_range_B_refined 11.16 r_long_range_B_other 11.16 r_dihedral_angle_1_deg 8.003 r_scangle_other 7.436 r_mcangle_it 7.186 r_mcangle_other 7.185 r_scbond_it 4.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.405 r_dihedral_angle_3_deg 18.113 r_dihedral_angle_4_deg 17.203 r_long_range_B_refined 11.16 r_long_range_B_other 11.16 r_dihedral_angle_1_deg 8.003 r_scangle_other 7.436 r_mcangle_it 7.186 r_mcangle_other 7.185 r_scbond_it 4.887 r_scbond_other 4.886 r_mcbond_it 4.394 r_mcbond_other 4.381 r_angle_refined_deg 1.881 r_angle_other_deg 1.744 r_chiral_restr 0.094 r_gen_planes_other 0.023 r_bond_refined_d 0.012 r_bond_other_d 0.01 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3420 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing