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Crystal Structure of the b1b2 domains from Human Neuropilin-1 in complex with a 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 295 0.1 M sodium malonate pH 6.0,
9% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.08 40.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.69 α = 90 b = 34.91 β = 102.2 c = 69.97 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 2021-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.55 42.57 100 1 1 6.8 45579
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.55 42.57 43313 2255 99.93 0.171 0.16933 0.20249 0.2106 RANDOM 27.85
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] 1.04 0.3 -1.18 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.351 r_dihedral_angle_4_deg 18.417 r_dihedral_angle_3_deg 13.195 r_dihedral_angle_1_deg 7.643 r_long_range_B_refined 5.896 r_long_range_B_other 5.895 r_scangle_other 4.356 r_scbond_it 2.817 r_scbond_other 2.817 r_mcangle_it 2.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.351 r_dihedral_angle_4_deg 18.417 r_dihedral_angle_3_deg 13.195 r_dihedral_angle_1_deg 7.643 r_long_range_B_refined 5.896 r_long_range_B_other 5.895 r_scangle_other 4.356 r_scbond_it 2.817 r_scbond_other 2.817 r_mcangle_it 2.647 r_mcangle_other 2.646 r_angle_refined_deg 1.879 r_mcbond_it 1.79 r_mcbond_other 1.789 r_angle_other_deg 1.453 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 2507 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing