☰ Navigation Tabs
Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QQM 2QQM, 2QQK experimental model PDB 2QQK 2QQM, 2QQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M HEPES, pH 7.5, 1.5M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 245.359 α = 90 b = 245.359 β = 90 c = 47.93 γ = 120
Symmetry Space Group P 3 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 PIXEL DECTRIS PILATUS 2M 2011-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 Diamond I04-1
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 2.7 81 99.4 45127 45127 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2QQM, 2QQK 2.7 81 -3 45078 42837 2241 99.18 0.20007 0.20007 0.19889 0.2028 0.22279 0.2251 RANDOM 68.168
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] 1.61 0.81 1.61 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.049 r_dihedral_angle_4_deg 17.694 r_dihedral_angle_3_deg 16.835 r_dihedral_angle_1_deg 7.096 r_angle_refined_deg 1.582 r_angle_other_deg 0.761 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.049 r_dihedral_angle_4_deg 17.694 r_dihedral_angle_3_deg 16.835 r_dihedral_angle_1_deg 7.096 r_angle_refined_deg 1.582 r_angle_other_deg 0.761 r_chiral_restr 0.083 r_bond_refined_d 0.009 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 4472 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 77
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction Aimless data scaling