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Crystal structure of Trk-A in complex with Staurosporin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286.15 Well volume: 30.0 uL
Well Ingredients:
Polymer: 10.0 %w/v PEG 3350
Buffer: 16.0 %v/v tacsimate (pH 8.00)
Organic (non-volatile): 10.0 %v/v Ethylene glycol
Additive: 0.025 M TCEP hydrochloride
Plate setup temperature: 13 C
Plate incubation temperature: 21 C
Drop volume from well: 0.2 uL
Drop protein volume: 0.4 uL (6.3mg/ml)
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.529 α = 90 b = 45.612 β = 127.06 c = 79.473 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 95 CCD RAYONIX MX-300 2014-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.000 CLSI 08ID-1
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 2.864 50 99.3 0.122 12.2 3.5 7577
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 2.864 2.98 95.4 0.756 2 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.864 45.3 7577 350 98.9 0.2204 0.2177 0.2774 0.2949 RANDOM 83.51
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] -4.4943 21.1248 17.9477 -13.4534
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.99 t_omega_torsion 2.61 t_angle_deg 0.85 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2110 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose BUSTER refinement HKL-2000 data reduction SCALEPACK data scaling BUSTER phasing