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The b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QQI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.3% Sodium-L ascorbate, 0.3% Choline Chloride, 0.3% D-Panthenol, 0.3% Pyridoxine hydrochloride, 0.3% Thiamine hydrochloride, 0.3% CHAPS, 0.3% CHAPSO, 0.3% Sodium glycocholate hydrate, 0.3% Taurocholic acid sodium salt hydrate, 100 mM Tris/Bicine, 10% PEG 20,000, 20% PEG 500 MME
Crystal Properties Matthews coefficient Solvent content 2.42 49.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.762 α = 90 b = 68.292 β = 90 c = 119.041 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 XE 16M 2024-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.667 59.521 67.8 0.32 0.324 0.053 0.998 9 37.1 30060
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.667 1.864 12.2 2.442 2.48 0.428 0.76 1.7 33.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.668 59.521 30060 1480 67.869 0.193 0.1909 0.2007 0.2403 0.2513 21.213
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] 0.125 -0.18 0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.512 r_dihedral_angle_6_deg 12.887 r_lrange_it 7.536 r_lrange_other 7.466 r_dihedral_angle_1_deg 7.254 r_dihedral_angle_2_deg 6.605 r_scangle_it 4.583 r_scangle_other 4.581 r_mcangle_other 3.698 r_mcangle_it 3.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.512 r_dihedral_angle_6_deg 12.887 r_lrange_it 7.536 r_lrange_other 7.466 r_dihedral_angle_1_deg 7.254 r_dihedral_angle_2_deg 6.605 r_scangle_it 4.583 r_scangle_other 4.581 r_mcangle_other 3.698 r_mcangle_it 3.697 r_scbond_it 2.72 r_scbond_other 2.72 r_mcbond_it 2.175 r_mcbond_other 2.173 r_angle_refined_deg 1.486 r_angle_other_deg 0.526 r_xyhbond_nbd_refined 0.221 r_symmetry_xyhbond_nbd_refined 0.201 r_symmetry_nbd_refined 0.194 r_symmetry_nbd_other 0.189 r_nbd_refined 0.188 r_nbtor_refined 0.177 r_nbd_other 0.16 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.012 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2478 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement DIALS data reduction STARANISO data scaling PHASER phasing