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VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VPF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.44 α = 90 b = 71.13 β = 105.28 c = 77.86 γ = 90
Symmetry Space Group C 1 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 160 CCD ADSC QUANTUM 1997-02-18 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1
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 1.7 30 99 0.052 8.3 7 47047 23.9
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 1.7 1.76 95.8 0.27 3.5 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT/NCS AVERAGING THROUGHOUT 1VPF 1.7 20 0.2 45678 2275 96.8 0.198 0.198 0.261 RANDOM 31.9
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] 1.905 -2.748 -4.0386 2.1336
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 28.8 x_scangle_it 6.3 x_mcangle_it 4.9 x_scbond_it 3.9 x_mcbond_it 2.4 x_angle_deg 1.76 x_improper_angle_d 0.99 x_bond_d 0.013 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 28.8 x_scangle_it 6.3 x_mcangle_it 4.9 x_scbond_it 3.9 x_mcbond_it 2.4 x_angle_deg 1.76 x_improper_angle_d 0.99 x_bond_d 0.013 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3090 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building X-PLOR refinement X-PLOR phasing