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Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor N-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]benzamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VRY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.1M Tris, 0.1M calcium acetate, 20% glycerol, 21% PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.09 60.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.72 α = 90 b = 96.05 β = 90 c = 181.65 γ = 90
Symmetry Space Group P 21 21 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 CCD RAYONIX MX225HE 2011-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.93 50 99.6 28358 28245 3 3 72.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.93 3.1 98
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3VRY 2.934 39.287 1.99 28245 28221 1411 99.6 0.2946 0.24 0.2372 0.2321 0.2946 0.2906 random 79.3655
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] 0.2207 -1.8386 1.618
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.807 f_angle_d 0.746 f_chiral_restr 0.058 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6959 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 64
Software Software Software Name Purpose ADSC data collection PHASER phasing PHENIX refinement XDS data reduction XDS data scaling