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Crystal structure of the exctracellular domain of the receptor tyrosine kinase, Kit
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 277 12% PEG 400, 0.2M KCl, 0.1M Na-Pi buffer, pH 6.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.88 57.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.249 α = 90 b = 162.249 β = 90 c = 67.586 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 QUANTUM 4 2006-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1000 NSLS X26C
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 50 99.8 0.076 11.7 11.7 13342 13342
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 3.11 100 0.17 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIRAS THROUGHOUT 3 27.07 13189 12521 650 99.86 0.25638 0.25435 0.2731 0.29505 0.2757 RANDOM 31.821
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] -0.76 -0.38 -0.76 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.886 r_dihedral_angle_3_deg 20.571 r_dihedral_angle_4_deg 12.511 r_dihedral_angle_1_deg 6.211 r_scangle_it 5.334 r_mcangle_it 4.056 r_scbond_it 3.596 r_mcbond_it 2.544 r_angle_refined_deg 1.848 r_symmetry_hbond_refined 0.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.886 r_dihedral_angle_3_deg 20.571 r_dihedral_angle_4_deg 12.511 r_dihedral_angle_1_deg 6.211 r_scangle_it 5.334 r_mcangle_it 4.056 r_scbond_it 3.596 r_mcbond_it 2.544 r_angle_refined_deg 1.848 r_symmetry_hbond_refined 0.357 r_nbtor_refined 0.339 r_symmetry_vdw_refined 0.334 r_nbd_refined 0.303 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.115 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3498 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 70
Software Software Software Name Purpose CNS refinement CBASS data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing REFMAC refinement