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Helix-loop-helix peptide (VS42-LR3) in complex with VEGF-A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VPF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 8 277 0.1M Tris-HCl pH 8.0, 0.2M NaCl, 2.5M Ammonium Sulfate, 0.04% NaN3
Crystal Properties Matthews coefficient Solvent content 2.49 50.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.982 α = 90 b = 42.982 β = 90 c = 309.665 γ = 120
Symmetry Space Group P 65 2 2
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 EIGER X 16M 2021-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9 SPring-8 BL41XU
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 1.45 44.24 100 0.06 0.061 0.014 0.999 22.3 20.4 31964
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 1.45 1.47 100 0.786 0.807 0.183 0.92 19.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.45 37.251 31791 1533 99.981 0.217 0.2156 0.2224 0.2449 0.251 RANDOM 27.699
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] 0.497 0.248 0.497 -1.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.517 r_dihedral_angle_6_deg 14.071 r_dihedral_angle_2_deg 9.013 r_lrange_it 8.907 r_lrange_other 8.866 r_scangle_it 7.197 r_scangle_other 7.193 r_dihedral_angle_1_deg 5.764 r_scbond_it 4.637 r_scbond_other 4.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.517 r_dihedral_angle_6_deg 14.071 r_dihedral_angle_2_deg 9.013 r_lrange_it 8.907 r_lrange_other 8.866 r_scangle_it 7.197 r_scangle_other 7.193 r_dihedral_angle_1_deg 5.764 r_scbond_it 4.637 r_scbond_other 4.633 r_mcangle_other 4.175 r_mcangle_it 4.174 r_mcbond_it 2.854 r_mcbond_other 2.846 r_angle_refined_deg 1.919 r_angle_other_deg 0.627 r_symmetry_xyhbond_nbd_refined 0.248 r_nbd_refined 0.207 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.155 r_nbd_other 0.155 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1117 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing