☰ Navigation Tabs
Crystal structure of VEGFR-1 domain 2 in presence of Zn
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FLT PDB ENTRY 1FLT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 VAPOR DIFFUSION METHOD, MOTHER LIQUOR:1MM VEGFR-1-D2,0.1%(W/V) DDM,4MM LAXAPHYCINE-A,5MM HEPES/NAOH PH 7.5. RESERVOIR:18% (W/V) PEG8000,100MM HEPES/NAOH PH 7.5, 18C
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.73 α = 90 b = 102.39 β = 90 c = 27.47 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 PIXEL DECTRIS PILATUS 6M CYLINDRICAL GRAZING INCIDENCE MIRROR BENT TO APPROXIMATE TO A TOROIDAL CURVATURE 2010-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.05 47.86 96.9 0.05 15.46 3.9 8564 27.29
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 2.06 2.13 83.8 0.16 3.97 2.3
Refinement Statistics Diffraction ID Structure Solution 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1FLT 2.055 47.865 1.94 8562 731 93.81 0.165 0.1628 0.1715 0.2053 0.2193 29.7
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 f_dihedral_angle_d 13.741 f_angle_d 1.091 f_chiral_restr 0.076 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 759 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALEPACK data scaling PHENIX phasing