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Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 289 10% PEG20000, 0.1M Bicine, 2% v/v dioxane
Crystal Properties Matthews coefficient Solvent content 2.77 55.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.25 α = 90 b = 139.52 β = 90 c = 106.04 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M 2013-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 86.5 99.5 0.059 10.8 3.4 59661
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.05 98.4 0.223 4.3 3.2
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 2QQJ 1.95 86.5 56630 3006 99.34 0.20576 0.20425 0.2106 0.23368 0.2388 RANDOM 26.756
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] 2.29 -1.79 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.852 r_dihedral_angle_4_deg 16.589 r_dihedral_angle_3_deg 13.207 r_dihedral_angle_1_deg 7.298 r_long_range_B_refined 4.245 r_long_range_B_other 4.245 r_mcangle_it 1.594 r_mcangle_other 1.594 r_scangle_other 1.549 r_angle_refined_deg 1.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.852 r_dihedral_angle_4_deg 16.589 r_dihedral_angle_3_deg 13.207 r_dihedral_angle_1_deg 7.298 r_long_range_B_refined 4.245 r_long_range_B_other 4.245 r_mcangle_it 1.594 r_mcangle_other 1.594 r_scangle_other 1.549 r_angle_refined_deg 1.463 r_angle_other_deg 0.923 r_mcbond_it 0.919 r_mcbond_other 0.912 r_scbond_it 0.91 r_scbond_other 0.908 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 5160 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction