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X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 28% w/v PEG3350, 0.2 M AmCl
Crystal Properties Matthews coefficient Solvent content 2.05 39.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.139 α = 90 b = 88.936 β = 96.73 c = 40.962 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 PIXEL DECTRIS PILATUS 6M-F 2015-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.52 40.68 95.4 0.048 1 22.8 6.6 41807
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 1.52 1.55 67.8 0.51 2.8 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.52 40.68 39714 2093 95.29 0.18264 0.1811 0.192 0.21298 0.2227 RANDOM 20.083
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] 0.46 -1.08 -1.57 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.801 r_dihedral_angle_4_deg 20.695 r_dihedral_angle_3_deg 12.594 r_dihedral_angle_1_deg 7.391 r_long_range_B_refined 5.172 r_long_range_B_other 5.171 r_scangle_other 2.541 r_angle_refined_deg 1.883 r_mcangle_it 1.651 r_mcangle_other 1.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.801 r_dihedral_angle_4_deg 20.695 r_dihedral_angle_3_deg 12.594 r_dihedral_angle_1_deg 7.391 r_long_range_B_refined 5.172 r_long_range_B_other 5.171 r_scangle_other 2.541 r_angle_refined_deg 1.883 r_mcangle_it 1.651 r_mcangle_other 1.651 r_scbond_it 1.626 r_scbond_other 1.625 r_angle_other_deg 1.543 r_mcbond_it 0.983 r_mcbond_other 0.983 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.009 r_gen_planes_other 0.008 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 2475 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing