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Helix-loop-helix peptide (M49) 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 5.6 293 0.2M NH4-AcOH pH 5.6, 14% PEG 3350, 20% 2-Propanol, 0.2M CaCl2,, 0.4M NaCl, 0.04% NaN3
Crystal Properties Matthews coefficient Solvent content 2.1 41.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.26 α = 90 b = 66.42 β = 90 c = 76.36 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 EIGER X 16M 2017-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8 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 47938
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 (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 1.46 44.24 47938 2518 99.92 0.21854 0.21691 0.2262 0.25038 0.2594 RANDOM 24.784
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] -1.27 2.52 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.971 r_dihedral_angle_4_deg 23.745 r_dihedral_angle_3_deg 14.384 r_dihedral_angle_1_deg 7.154 r_long_range_B_refined 7.132 r_long_range_B_other 7.086 r_scangle_other 5.053 r_mcangle_other 3.684 r_mcangle_it 3.683 r_scbond_it 3.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.971 r_dihedral_angle_4_deg 23.745 r_dihedral_angle_3_deg 14.384 r_dihedral_angle_1_deg 7.154 r_long_range_B_refined 7.132 r_long_range_B_other 7.086 r_scangle_other 5.053 r_mcangle_other 3.684 r_mcangle_it 3.683 r_scbond_it 3.31 r_scbond_other 3.276 r_mcbond_it 2.47 r_mcbond_other 2.467 r_angle_refined_deg 1.708 r_angle_other_deg 1.39 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2196 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing