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Crystal Structure of Human Neuropilin-1 b1 Domain mutant - Y297A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Precipitant of 20% PEG4000, 0.1M Tris (pH 8.5), 0.2M Lithium Sulfate.
Protein concentration used is 10 mg/mL, mixed 1:1 with precipitant for hanging drop over reservoir of 1 mL.
Crystal Properties Matthews coefficient Solvent content 3.31 62.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.076 α = 90 b = 80.076 β = 90 c = 62.198 γ = 120
Symmetry Space Group P 32 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 6M 2019-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9724 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.56 46.35 100 0.019 0.026 0.019 0.999 17.6 1.9 33072
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.59 100 0.18 0.254 0.18 0.908 1.9
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 1KEX 1.56 46.35 31397 1654 99.94 0.1811 0.1796 0.1906 0.2088 0.2116 RANDOM 25.189
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] 0.16 0.08 0.16 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.856 r_dihedral_angle_4_deg 19.876 r_dihedral_angle_3_deg 11.587 r_dihedral_angle_1_deg 7.78 r_angle_refined_deg 1.965 r_angle_other_deg 1.476 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.856 r_dihedral_angle_4_deg 19.876 r_dihedral_angle_3_deg 11.587 r_dihedral_angle_1_deg 7.78 r_angle_refined_deg 1.965 r_angle_other_deg 1.476 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1232 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction