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Dcps in complex with covalent inhibitor targeting Tyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XMM PDB ENTRY 1XMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 295 1:1 protein (4 mg/mL in 25 mM NaCl, 20 mM Tris-HCl, pH 8.0, 1 mM TCEP) to precipitant (23-25% PEG3350, 0.1 M potassium phosphate monobasic, 0.05 M sodium chloride, 26% glycerol, crystals soaked in 1 mM inhibitor overnight, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.42 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.25 α = 90 b = 105.23 β = 90 c = 139.96 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 PIXEL DECTRIS PILATUS 6M 2013-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
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 3.2 82.03 93.9 0.317 3.3 23629 77.55
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1XMM 3.21 33.89 20868 1069 83.25 0.214 0.2107 0.2634 0.2763 0.2959 RANDOM 105.62
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] 6.163 1.1579 -7.3208
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.03 t_omega_torsion 2.59 t_angle_deg 1.23 t_bond_d 0.011 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 23.03 t_omega_torsion 2.59 t_angle_deg 1.23 t_bond_d 0.011 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 9561 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 43
Software Software Software Name Purpose Jdirect data collection MOLREP phasing BUSTER refinement autoPROC data scaling CCP4 data scaling