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Crystal structure of an engineered human autonomous VH Domain in complex with VEGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 10 %(w/v) PEG 4000, 20 %(w/v) Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.727 α = 90 b = 132.908 β = 90 c = 175.481 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 CCD MARMOSAIC 225 mm CCD 2008-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 50 92.5 0.058 0.058 19.5 4 44934 47.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 94.9 0.326 3.6 4 4512
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.41 50 44896 42491 2277 91.65 0.19548 0.19341 0.1887 0.23332 0.2265 RANDOM 40.099
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] 0.99 0.31 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.238 r_dihedral_angle_4_deg 20.903 r_dihedral_angle_3_deg 17.127 r_dihedral_angle_1_deg 8.562 r_scangle_it 5.433 r_scbond_it 3.414 r_mcangle_it 2.358 r_mcbond_it 1.243 r_angle_refined_deg 1.014 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.238 r_dihedral_angle_4_deg 20.903 r_dihedral_angle_3_deg 17.127 r_dihedral_angle_1_deg 8.562 r_scangle_it 5.433 r_scbond_it 3.414 r_mcangle_it 2.358 r_mcbond_it 1.243 r_angle_refined_deg 1.014 r_chiral_restr 0.082 r_gen_planes_refined 0.012 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6911 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms
Software Software Software Name Purpose DNA data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling