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Crystal structure of the human BTK kinase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 equal volumes of well solution (0.2 M Na Malonate pH 7.0, 20% PEG 3350, 3% 6-aminocaproic acid) and protein solution (8 mg/mL in 100 mM NaCl, 10 mM Tris-HCL, pH8.5, 1mM TCEP) , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.602 α = 90 b = 103.493 β = 90 c = 117.564 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 ADSC QUANTUM 315 2008-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 50 99.2 0.063 20.6 4.7 51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 98.1 0.53 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1K2P 2.3 47.35 26031 23279 2542 99.2 0.22776 0.22776 0.22221 0.27791 0.2833 RANDOM 53.508
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] -0.08 -1.67 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.993 r_dihedral_angle_4_deg 19.564 r_dihedral_angle_3_deg 15.535 r_dihedral_angle_1_deg 6.82 r_scangle_it 3.622 r_mcangle_it 3.588 r_scbond_it 2.524 r_mcbond_it 2.429 r_angle_refined_deg 1.18 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.993 r_dihedral_angle_4_deg 19.564 r_dihedral_angle_3_deg 15.535 r_dihedral_angle_1_deg 6.82 r_scangle_it 3.622 r_mcangle_it 3.588 r_scbond_it 2.524 r_mcbond_it 2.429 r_angle_refined_deg 1.18 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4195 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling