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Crystal Structure of the a2b1b2 Domains from Human Neuropilin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QQI 2QQI (b1b2 domains), 2QQK (a2 domain) experimental model PDB 2QQK 2QQI (b1b2 domains), 2QQK (a2 domain)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 297 0.1 M MES, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.33 47.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.177 α = 90 b = 68.178 β = 102.1 c = 66.613 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 CCD MARMOSAIC 325 mm CCD 2006-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979 SSRL BL11-1
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 50 97.5 0.086 13.8 3.5 30901 30.9
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 2.07 88.7 0.322 3.2 3 2794
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 2QQI (b1b2 domains), 2QQK (a2 domain) 2 20 29213 1558 97.55 0.186 0.183 0.19 0.243 0.2492 RANDOM 36.27
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] -2.38 2.16 -1.22 4.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.335 r_dihedral_angle_4_deg 18.699 r_dihedral_angle_3_deg 13.546 r_dihedral_angle_1_deg 6.631 r_mcangle_it 4.666 r_scangle_it 4.572 r_mcbond_it 3.511 r_scbond_it 3.314 r_angle_refined_deg 1.455 r_angle_other_deg 0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.335 r_dihedral_angle_4_deg 18.699 r_dihedral_angle_3_deg 13.546 r_dihedral_angle_1_deg 6.631 r_mcangle_it 4.666 r_scangle_it 4.572 r_mcbond_it 3.511 r_scbond_it 3.314 r_angle_refined_deg 1.455 r_angle_other_deg 0.843 r_mcbond_other 0.843 r_symmetry_vdw_refined 0.234 r_symmetry_vdw_other 0.213 r_nbd_other 0.195 r_nbd_refined 0.185 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.126 r_metal_ion_refined 0.105 r_nbtor_other 0.096 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3456 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 101
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