☰ Navigation Tabs
Structure of cyclin-dependent kinase 2 with small-molecule ligand 3-(4,7-dichloro-1H-indol-3-yl)prop-2-yn-1-ol (AT17833) in an alternate binding site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FP5 PDB ENTRY 5FP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 PROTEIN CONCENTRATION: 13.6 MG/ML, pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.25 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.917 α = 90 b = 72.214 β = 90 c = 72.198 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 93 CCD RIGAKU CCD MIRROR 2007-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 1.85 32.3 94.3 0.04 13.2 24694 -3.7 27.83
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 1.85 1.92 63.3 0.22 2
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 PDB ENTRY 5FP5 1.85 32.29 23282 1142 94.28 0.2086 0.207 0.2403 0.2196 RANDOM 30.85
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] 1.9128 -4.6795 2.7667
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.51 t_omega_torsion 5.72 t_angle_deg 0.65 t_bond_d 0.012 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.51 t_omega_torsion 5.72 t_angle_deg 0.65 t_bond_d 0.012 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 2176 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 30
Software Software Software Name Purpose BUSTER refinement d*TREK data reduction DTSCALE data scaling CSEARCH phasing