☰ Navigation Tabs
Crystal Structure of human vascular endothelial growth factor-B: Identification of amino acids important for angiogeninc activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VPF PDB ENTRY 2VPF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 0.1M HEPES (PH 6.8), 0.5M AMMONIUM SULPHATE 50%, MPD
Crystal Properties Matthews coefficient Solvent content 3.4 63.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.806 α = 90 b = 120.806 β = 90 c = 39.826 γ = 120
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 CCD MIRRORS 2003-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 2.48 40 97.4 0.096 12.9 9.1 12054 43.1
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 2.48 2.57 99.3 0.63 2.4 10.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VPF 2.48 40 10937 712 90.7 0.286 0.286 0.2796 0.31 RANDOM 40.2
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.8 c_angle_deg 1.6 c_improper_angle_d 1.11 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.8 c_angle_deg 1.6 c_improper_angle_d 1.11 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1392 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 8
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing