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Crystal Structure of the a2b1b2 Domains from Human Neuropilin-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QQJ 2QQJ (b1b2 domains), 2QQK (a2 domain) experimental model PDB 2QQK 2QQJ (b1b2 domains), 2QQK (a2 domain)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 297 0.1 M Hepes, 10% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.08 60.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.093 α = 90 b = 192.909 β = 90.08 c = 66.169 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 ADSC QUANTUM 210 2007-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.00 ALS 5.0.1
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 2.3 50 94.5 0.056 14 4.2 52659
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 2.3 2.38 85.6 0.344 3.7 4.1 4766
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2QQJ (b1b2 domains), 2QQK (a2 domain) 2.3 20 49667 2679 94.47 0.188 0.185 0.239 0.2469 RANDOM 31.764
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] 0.27 0.02 0.08 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.285 r_dihedral_angle_4_deg 19.607 r_dihedral_angle_3_deg 14.393 r_dihedral_angle_1_deg 7.149 r_scangle_it 4.605 r_mcangle_it 4.345 r_scbond_it 3.348 r_mcbond_it 3.108 r_angle_refined_deg 1.44 r_angle_other_deg 0.897
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.285 r_dihedral_angle_4_deg 19.607 r_dihedral_angle_3_deg 14.393 r_dihedral_angle_1_deg 7.149 r_scangle_it 4.605 r_mcangle_it 4.345 r_scbond_it 3.348 r_mcbond_it 3.108 r_angle_refined_deg 1.44 r_angle_other_deg 0.897 r_mcbond_other 0.861 r_symmetry_vdw_other 0.204 r_nbd_other 0.195 r_nbd_refined 0.179 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.153 r_symmetry_vdw_refined 0.143 r_symmetry_hbond_refined 0.14 r_metal_ion_refined 0.109 r_chiral_restr 0.087 r_nbtor_other 0.083 r_bond_refined_d 0.013 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 6813 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 34
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