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Crystal structure of the extracellular domain of Kit in complex with stem cell factor (SCF)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EXZ PDB ENTRY 1EXZ and 2EC8 experimental model PDB 2EC8 PDB ENTRY 1EXZ and 2EC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 277 8-12% PEG 8000, 5-8% ethylene glycol, 0.2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.46 72.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 269.477 α = 90 b = 52.072 β = 108 c = 189.791 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 100 CCD ADSC QUANTUM 210 1999-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.249999 NSLS X25
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 3.5 50 98.5 0.061 14.9 3.55 31962 31962 54.6
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 3.5 3.63 91.4 0.176 6.6
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 (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 1EXZ and 2EC8 3.5 38.96 31945 31945 1594 98.3 0.245 0.245 0.2206 0.294 0.2641 RANDOM 78.1
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] -7.15 28.76 23.73 -16.58
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.1 c_scangle_it 16.82 c_mcangle_it 11.8 c_scbond_it 11.63 c_mcbond_it 7.41 c_angle_deg 1.7 c_improper_angle_d 1.02 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.1 c_scangle_it 16.82 c_mcangle_it 11.8 c_scbond_it 11.63 c_mcbond_it 7.41 c_angle_deg 1.7 c_improper_angle_d 1.02 c_bond_d 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9084 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 84
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling PHASER phasing