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Structure of VEGF complexed to a Fab containing TYR and SER in the CDRs
Crystallization Crystal Properties Matthews coefficient Solvent content 3.07 59.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.453 α = 90 b = 90.218 β = 90.85 c = 205.558 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2
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 3.5 50 96.1 0.097 10.7 3.3 71940
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 3.5 3.63 93.4 0.444 2.9 6873
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-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 3.5 20 68755 3496 96.13 0.292 0.292 0.291 0.2581 0.312 0.273 RANDOM 65.484
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] 4.8 -3.56 0.36 -5.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.478 r_dihedral_angle_3_deg 18.479 r_dihedral_angle_4_deg 12.205 r_dihedral_angle_1_deg 5.494 r_mcangle_it 3.626 r_mcbond_it 2.959 r_scangle_it 2.611 r_scbond_it 1.602 r_angle_refined_deg 1.037 r_angle_other_deg 0.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.478 r_dihedral_angle_3_deg 18.479 r_dihedral_angle_4_deg 12.205 r_dihedral_angle_1_deg 5.494 r_mcangle_it 3.626 r_mcbond_it 2.959 r_scangle_it 2.611 r_scbond_it 1.602 r_angle_refined_deg 1.037 r_angle_other_deg 0.712 r_symmetry_vdw_other 0.38 r_symmetry_vdw_refined 0.337 r_symmetry_hbond_refined 0.277 r_nbd_refined 0.193 r_nbd_other 0.181 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.149 r_mcbond_other 0.105 r_nbtor_other 0.082 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_xyhbond_nbd_other 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32356 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction