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D-Protein RFX-V2 Bound to the VEGFR1 Domain 3 Site on VEGF-A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.2 magnesium chloride, Bis-Tris, PEG3350
Crystal Properties Matthews coefficient Solvent content 3.22 61.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.85 α = 90 b = 120.437 β = 90 c = 120.437 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 PIXEL DECTRIS PILATUS3 6M 2018-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1
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 2.9 120.44 99.9 0.061 0.064 0.018 1 25.7 12.8 22242
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 2.9 3.08 99.9 1.1 1.147 0.32 0.775 12.7
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 3QTK 2.9 58.52 21151 1033 99.83 0.2651 0.2627 0.2654 0.3153 0.3194 RANDOM 129.323
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] -7.59 4.5 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.879 r_dihedral_angle_3_deg 20.191 r_dihedral_angle_4_deg 18.171 r_dihedral_angle_1_deg 10.839 r_angle_refined_deg 1.795 r_angle_other_deg 1.067 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.879 r_dihedral_angle_3_deg 20.191 r_dihedral_angle_4_deg 18.171 r_dihedral_angle_1_deg 10.839 r_angle_refined_deg 1.795 r_angle_other_deg 1.067 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4909 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing