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Crystal structure of DLK (kinase domain)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DTC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 292 0.2 M magnesium acetate, 20% PEG 3350, 0.1 M HEPES pH 7.7
Crystal Properties Matthews coefficient Solvent content 1.94 36.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.289 α = 90 b = 39.713 β = 104.73 c = 59.907 γ = 90
Symmetry Space Group P 1 21 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 315 2010-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
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 1.7 75 100 0.072 9.2 3.7 29149 21.19
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 1.7 1.76 100 0.629 3.6 2881
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3DTC 1.7 46.36 29003 1467 99.98 0.1871 0.1851 0.2246 0.2269 RANDOM 26.21
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] 4.5372 0.6646 -2.6997 -1.8376
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.32 t_omega_torsion 3.09 t_angle_deg 1.02 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.32 t_omega_torsion 3.09 t_angle_deg 1.02 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2245 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling BUSTER-TNT refinement PDB_EXTRACT data extraction PHASER phasing HKL-2000 data reduction