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Crystal Structure of the b1b2 Domains from Human Neuropilin-1
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, SITTING DROP 292 20% PEG 3350, 0.2 M Sodium Fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.28 46.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.92 α = 90 b = 66.979 β = 90 c = 74.679 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 ADSC QUANTUM 315 2003-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
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 1.8 50 97.6 0.05 26.9 4.6 30653 26.2
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 1.8 1.86 99.3 0.515 3.2 4.6 3047
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 1.8 20 29018 1526 97.67 0.161 0.159 0.1693 0.201 0.2056 RANDOM 26.584
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] -1.58 0.32 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.853 r_dihedral_angle_4_deg 15.348 r_dihedral_angle_3_deg 12.126 r_dihedral_angle_1_deg 6.553 r_scangle_it 4.711 r_mcangle_it 3.904 r_scbond_it 3.519 r_mcbond_it 3.397 r_angle_refined_deg 1.5 r_angle_other_deg 0.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.853 r_dihedral_angle_4_deg 15.348 r_dihedral_angle_3_deg 12.126 r_dihedral_angle_1_deg 6.553 r_scangle_it 4.711 r_mcangle_it 3.904 r_scbond_it 3.519 r_mcbond_it 3.397 r_angle_refined_deg 1.5 r_angle_other_deg 0.894 r_mcbond_other 0.708 r_symmetry_vdw_other 0.256 r_symmetry_vdw_refined 0.233 r_nbd_other 0.203 r_nbd_refined 0.188 r_nbtor_refined 0.183 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.096 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2514 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 6
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