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Structural basis for the function of two anti-VEGF receptor antibodies
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M imidazole, pH 6.5; 0.1 M CaCl2, 40% PEG 1500, 10% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.66 53.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.864 α = 90 b = 64.864 β = 90 c = 263.161 γ = 120
Symmetry Space Group P 32 2 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 2009-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 1.0 APS 31-ID
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 3.2 55 98.6 0.099 20.8 10.2 11240 11083 -3 91.7
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 3.2 3.37 98.8 0.688 3.2 10.5 1602
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 3.2 54.96 11324 10548 522 97.76 0.27698 0.27431 0.277 0.33187 0.3267 RANDOM 124.403
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] 4.97 2.48 4.97 -7.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.68 r_dihedral_angle_3_deg 11.897 r_dihedral_angle_4_deg 11.13 r_dihedral_angle_1_deg 4.402 r_angle_refined_deg 0.754 r_angle_other_deg 0.686 r_scangle_it 0.171 r_scbond_it 0.095 r_mcangle_it 0.071 r_chiral_restr 0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.68 r_dihedral_angle_3_deg 11.897 r_dihedral_angle_4_deg 11.13 r_dihedral_angle_1_deg 4.402 r_angle_refined_deg 0.754 r_angle_other_deg 0.686 r_scangle_it 0.171 r_scbond_it 0.095 r_mcangle_it 0.071 r_chiral_restr 0.046 r_mcbond_it 0.037 r_mcbond_other 0.006 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4104 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling