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Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QQJ 2QQJ (b1b2 domains), 2FJH (antibody), 1NT0 (a2 domain) experimental model PDB 2FJH 2QQJ (b1b2 domains), 2FJH (antibody), 1NT0 (a2 domain) experimental model PDB 1NT0 2QQJ (b1b2 domains), 2FJH (antibody), 1NT0 (a2 domain)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 297 0.1 M Hepes, 22% polyacrylic acid 5100, 0.02 M MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.16 61.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.277 α = 90 b = 105.873 β = 98.83 c = 92.4 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315 2006-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.75 50 99.6 0.104 10.9 4.2 36321 75.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.85 100 0.527 3.3 4.2 3599
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 2QQJ (b1b2 domains), 2FJH (antibody), 1NT0 (a2 domain) 2.75 30 34487 1830 98.99 0.189 0.186 0.1888 0.243 0.2384 RANDOM 74.912
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] 2.09 -2.82 4.17 -7.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.051 r_dihedral_angle_3_deg 16.882 r_dihedral_angle_4_deg 14.513 r_dihedral_angle_1_deg 6.807 r_mcangle_it 4.297 r_scangle_it 4.212 r_mcbond_it 3.256 r_scbond_it 2.917 r_angle_refined_deg 1.258 r_angle_other_deg 0.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.051 r_dihedral_angle_3_deg 16.882 r_dihedral_angle_4_deg 14.513 r_dihedral_angle_1_deg 6.807 r_mcangle_it 4.297 r_scangle_it 4.212 r_mcbond_it 3.256 r_scbond_it 2.917 r_angle_refined_deg 1.258 r_angle_other_deg 0.826 r_mcbond_other 0.504 r_symmetry_vdw_other 0.217 r_nbd_refined 0.193 r_nbd_other 0.188 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.175 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.12 r_nbtor_other 0.084 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7593 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction