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X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 30% w/v PEG3350, 0.2 M AmCl
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.525 α = 90 b = 88.945 β = 91.61 c = 41.7 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 1.38 41.5 98 0.137 0.993 7.4 6.5 60739
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 1.38 1.42 82.5 0.854 1.4 4.7
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 1KEX 1.6 44.47 37803 1935 99.66 0.14793 0.14591 0.1591 0.18705 0.2 RANDOM 13.416
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] -0.3 -0.03 0.02 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_dihedral_angle_4_deg 16.392 r_dihedral_angle_3_deg 12.04 r_dihedral_angle_1_deg 7.087 r_long_range_B_refined 6.213 r_long_range_B_other 5.883 r_scangle_other 3.9 r_scbond_it 2.56 r_scbond_other 2.559 r_angle_refined_deg 2.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_dihedral_angle_4_deg 16.392 r_dihedral_angle_3_deg 12.04 r_dihedral_angle_1_deg 7.087 r_long_range_B_refined 6.213 r_long_range_B_other 5.883 r_scangle_other 3.9 r_scbond_it 2.56 r_scbond_other 2.559 r_angle_refined_deg 2.117 r_mcangle_it 1.963 r_mcangle_other 1.963 r_angle_other_deg 1.366 r_mcbond_it 1.36 r_mcbond_other 1.352 r_chiral_restr 0.131 r_bond_refined_d 0.024 r_gen_planes_refined 0.014 r_bond_other_d 0.007 r_gen_planes_other 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 2501 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing