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Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QU5 PDB ENTRY 2QU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2M potassium formate, 20% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.46 50.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.04 α = 90 b = 71.15 β = 90 c = 196.02 γ = 90
Symmetry Space Group I 2 2 2
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 TOROIDAL ZERODUR MIRROR 2009-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93300 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 44.99 99.8 0.088 0.078 13.2 4.7 11982 11958 65.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.67 2.81 98.5 0.506 0.441 3.2 4.2 1669
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 (All) 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 2QU5 2.7 44.99 11021 10998 551 99.79 0.19739 0.19739 0.19431 0.2068 0.26018 0.2545 RANDOM 26.129
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] 0.09 1.14 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.976 r_dihedral_angle_4_deg 20.508 r_dihedral_angle_3_deg 19.825 r_dihedral_angle_1_deg 7.077 r_scangle_it 2.727 r_scbond_it 1.584 r_angle_refined_deg 1.46 r_mcangle_it 1.086 r_angle_other_deg 0.64 r_mcbond_it 0.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.976 r_dihedral_angle_4_deg 20.508 r_dihedral_angle_3_deg 19.825 r_dihedral_angle_1_deg 7.077 r_scangle_it 2.727 r_scbond_it 1.584 r_angle_refined_deg 1.46 r_mcangle_it 1.086 r_angle_other_deg 0.64 r_mcbond_it 0.547 r_mcbond_other 0.094 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2290 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 25
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement iMOSFLM data reduction SCALA data scaling PHENIX phasing