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Structural basis for the function of two anti-VEGF receptor antibodies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VL5 PDB ENTRY 1VL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 100 mM CdCl2, 100 mM Na acetate, pH 4.6, 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.84 56.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.937 α = 90 b = 112.13 β = 90 c = 156.971 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 CCD ADSC QUANTUM 4 2009-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 1.00 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 40 98.2 0.124 13.7 7.2 35617 34976 -3
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 2.2 2.32 97.7 0.619 3.2 7.3
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 (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 PDB ENTRY 1VL5 2.2 33.79 35710 33185 1790 97.94 0.20623 0.20338 0.2024 0.25943 0.255 RANDOM 22.485
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] 0.31 0.67 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.143 r_dihedral_angle_3_deg 16.53 r_dihedral_angle_4_deg 16.229 r_dihedral_angle_1_deg 6.973 r_scangle_it 2.614 r_scbond_it 1.705 r_angle_refined_deg 1.495 r_mcangle_it 1.024 r_mcbond_it 0.655 r_metal_ion_refined 0.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.143 r_dihedral_angle_3_deg 16.53 r_dihedral_angle_4_deg 16.229 r_dihedral_angle_1_deg 6.973 r_scangle_it 2.614 r_scbond_it 1.705 r_angle_refined_deg 1.495 r_mcangle_it 1.024 r_mcbond_it 0.655 r_metal_ion_refined 0.542 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.251 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.181 r_symmetry_metal_ion_refined 0.093 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4187 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 48
Software Software Software Name Purpose APS data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling