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Structural Basis for Ligand Binding and Heparin Mediated Activation of Neuropilin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KEX PDB entry 1KEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 291 100mM HEPES pH 7.6, 10% PEG 20K, 7% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.95 58.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.094 α = 90 b = 92.221 β = 90 c = 120.115 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2006-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 1.38 CAMD GCPCC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.4 50 16862
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 PDB entry 1KEX 2.4 29.37 15556 823 94.94 0.20402 0.20138 0.1941 0.25178 0.2405 RANDOM 57.395
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] -0.4 0.49 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.824 r_dihedral_angle_4_deg 19.322 r_dihedral_angle_3_deg 17.661 r_dihedral_angle_1_deg 7.356 r_scangle_it 1.956 r_angle_refined_deg 1.405 r_scbond_it 1.302 r_mcangle_it 0.92 r_mcbond_it 0.563 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.824 r_dihedral_angle_4_deg 19.322 r_dihedral_angle_3_deg 17.661 r_dihedral_angle_1_deg 7.356 r_scangle_it 1.956 r_angle_refined_deg 1.405 r_scbond_it 1.302 r_mcangle_it 0.92 r_mcbond_it 0.563 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.185 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2510 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing