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X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 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 7.9 289 18%PEG3350+0.2M NH4Cl
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.789 α = 90 b = 89.568 β = 98.57 c = 41.385 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 2015-07-30 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 1.6 40.92 97 0.047 0.998 10.5 3.1 37578
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 1.6 1.63 75.3 0.442 2 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1kex 1.6 44.78 35677 1853 96.88 0.16219 0.16056 0.19304 0.1995 RANDOM 19.591
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] 0.1 -1.51 -0.01 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.434 r_dihedral_angle_4_deg 19.489 r_dihedral_angle_3_deg 11.998 r_dihedral_angle_1_deg 7.188 r_long_range_B_refined 5.327 r_long_range_B_other 5.326 r_scangle_other 3.593 r_scbond_it 2.331 r_scbond_other 2.33 r_mcangle_it 2.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.434 r_dihedral_angle_4_deg 19.489 r_dihedral_angle_3_deg 11.998 r_dihedral_angle_1_deg 7.188 r_long_range_B_refined 5.327 r_long_range_B_other 5.326 r_scangle_other 3.593 r_scbond_it 2.331 r_scbond_other 2.33 r_mcangle_it 2.153 r_mcangle_other 2.152 r_angle_refined_deg 1.864 r_angle_other_deg 1.479 r_mcbond_it 1.456 r_mcbond_other 1.452 r_chiral_restr 0.127 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 2489 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing