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X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 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% w/v PEG3350, 0.2M NH4Cl
Crystal Properties Matthews coefficient Solvent content 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.59 α = 90 b = 90.48 β = 99.64 c = 81.89 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 2015-05-18 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 1.9 41 99.9 0.121 0.995 7.7 3.7 47057
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 1.9 1.95 99.9 1.086 1.1 3.7
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 2.1 80.73 33165 1728 99.78 0.18369 0.18157 0.1876 0.2232 0.2288 RANDOM 22.386
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] -0.99 -0.59 -0.1 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.78 r_dihedral_angle_4_deg 15.136 r_dihedral_angle_3_deg 12.535 r_dihedral_angle_1_deg 6.852 r_long_range_B_refined 4.283 r_long_range_B_other 4.283 r_scangle_other 2.182 r_mcangle_it 1.716 r_mcangle_other 1.715 r_angle_refined_deg 1.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.78 r_dihedral_angle_4_deg 15.136 r_dihedral_angle_3_deg 12.535 r_dihedral_angle_1_deg 6.852 r_long_range_B_refined 4.283 r_long_range_B_other 4.283 r_scangle_other 2.182 r_mcangle_it 1.716 r_mcangle_other 1.715 r_angle_refined_deg 1.517 r_scbond_it 1.29 r_scbond_other 1.29 r_angle_other_deg 1.218 r_mcbond_it 0.991 r_mcbond_other 0.988 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.007 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 4953 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing