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Crystal Structure of the Fab YADS1 Complexed with h-VEGF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VPF The VEGF from pdb entry 1VPF. The Fab from an in-house determined structure.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 PEG 3350, ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.269 α = 90 b = 76.269 β = 105.77 c = 112.497 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 4 2003-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
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 2.6 50 99.9 0.078 0.078 16.8 3.7 41883 41828 -3 54.378
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 99.1 0.423 0.423 2.4 3.5 4162
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 The VEGF from pdb entry 1VPF. The Fab from an in-house determined structure. 2.6 20 39704 39617 2105 99.78 0.21478 0.2147 0.21172 0.2177 0.27105 0.2727 RANDOM 25.123
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] -2.16 -2.47 0.56 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.33 r_scangle_it 4.544 r_mcangle_it 4.351 r_scbond_it 3.06 r_mcbond_it 2.827 r_angle_refined_deg 1.342 r_angle_other_deg 0.815 r_symmetry_vdw_refined 0.265 r_nbd_other 0.222 r_symmetry_vdw_other 0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.33 r_scangle_it 4.544 r_mcangle_it 4.351 r_scbond_it 3.06 r_mcbond_it 2.827 r_angle_refined_deg 1.342 r_angle_other_deg 0.815 r_symmetry_vdw_refined 0.265 r_nbd_other 0.222 r_symmetry_vdw_other 0.214 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.173 r_nbtor_other 0.086 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7994 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing