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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 293 200 mM magnesium formate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.84 33.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.541 α = 90 b = 34.592 β = 117.208 c = 70.226 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 EIGER2 XE 16M 2024-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 1.568 58.278 66.7 0.265 0.272 0.061 0.998 7.5 19.6 26510
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 1.568 1.796 10 2.028 2.086 0.485 0.592 1.6 18.4
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 1.569 58.278 26509 1509 66.807 0.175 0.1708 0.1806 0.2388 0.2463 20.333
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] 0.005 -0.013 -0.123 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.65 r_dihedral_angle_3_deg 13.11 r_dihedral_angle_2_deg 8.582 r_dihedral_angle_1_deg 7.956 r_lrange_it 6.81 r_lrange_other 6.724 r_scangle_it 4.784 r_scangle_other 4.782 r_scbond_it 3.088 r_scbond_other 3.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.65 r_dihedral_angle_3_deg 13.11 r_dihedral_angle_2_deg 8.582 r_dihedral_angle_1_deg 7.956 r_lrange_it 6.81 r_lrange_other 6.724 r_scangle_it 4.784 r_scangle_other 4.782 r_scbond_it 3.088 r_scbond_other 3.086 r_mcangle_it 3.049 r_mcangle_other 3.048 r_mcbond_it 1.946 r_mcbond_other 1.946 r_angle_refined_deg 1.526 r_angle_other_deg 0.53 r_symmetry_xyhbond_nbd_refined 0.241 r_nbd_other 0.225 r_xyhbond_nbd_refined 0.223 r_symmetry_nbd_refined 0.215 r_nbd_refined 0.199 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.18 r_xyhbond_nbd_other 0.132 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.039 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2528 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction STARANISO data scaling PHASER phasing