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Neuropilin1-b1 domain in complex with EG01377, 0.9 Angstrom structure
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 277.15 16 % w/v PEG3350 and 200 mM ammonium chloride
Crystal Properties Matthews coefficient Solvent content 2.4 48.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.44 α = 90 b = 43.44 β = 90 c = 91.23 γ = 90
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 PILATUS3 6M 2014-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.813010 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 0.9 43.44 94.5 0.057 0.998 10.55 3.3 117690
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.9 0.95 70.7 0.478 0.795
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 0.9 43.44 111866 6027 94.67 0.11015 0.10894 0.1085 0.13207 0.132 RANDOM 16.789
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.593 r_sphericity_free 34.773 r_dihedral_angle_4_deg 18.625 r_dihedral_angle_3_deg 14.861 r_sphericity_bonded 13.469 r_rigid_bond_restr 9.893 r_dihedral_angle_1_deg 7.652 r_long_range_B_refined 6.334 r_long_range_B_other 4.551 r_scangle_other 3.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.593 r_sphericity_free 34.773 r_dihedral_angle_4_deg 18.625 r_dihedral_angle_3_deg 14.861 r_sphericity_bonded 13.469 r_rigid_bond_restr 9.893 r_dihedral_angle_1_deg 7.652 r_long_range_B_refined 6.334 r_long_range_B_other 4.551 r_scangle_other 3.405 r_angle_other_deg 3.282 r_scbond_it 3.011 r_scbond_other 3.009 r_angle_refined_deg 2.647 r_mcangle_it 1.576 r_mcangle_other 1.575 r_mcbond_it 1.2 r_mcbond_other 1.197 r_chiral_restr 0.104 r_bond_refined_d 0.02 r_gen_planes_other 0.015 r_gen_planes_refined 0.012 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1261 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing