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Room Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HCL BACKBONE OF CYCLIN-DEPENDENT KINASE 2 (PDB entry 1HCL)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 PEG4000, sodium acetate, Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.55 α = 90 b = 61.44 β = 103.06 c = 45.41 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE MARRESEARCH Mirrors 1996-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.1 MPG/DESY, HAMBURG BW6
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 26.2 94 0.106 2.8 25896 24342 15.2
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 2.11 84.9 0.111 1.7
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 BACKBONE OF CYCLIN-DEPENDENT KINASE 2 (PDB entry 1HCL) 2 26 23092 1247 93.68 0.19487 0.19254 0.2015 0.23675 0.2419 RANDOM 27.212
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] -2.27 -1.32 2.2 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.714 r_dihedral_angle_1_deg 4.069 r_scangle_it 3.805 r_scbond_it 2.34 r_mcangle_it 1.649 r_angle_refined_deg 1.52 r_angle_other_deg 1.287 r_mcbond_it 0.926 r_symmetry_hbond_refined 0.465 r_nbd_refined 0.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.714 r_dihedral_angle_1_deg 4.069 r_scangle_it 3.805 r_scbond_it 2.34 r_mcangle_it 1.649 r_angle_refined_deg 1.52 r_angle_other_deg 1.287 r_mcbond_it 0.926 r_symmetry_hbond_refined 0.465 r_nbd_refined 0.248 r_symmetry_vdw_other 0.226 r_nbd_other 0.224 r_xyhbond_nbd_refined 0.215 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_other 0.145 r_symmetry_hbond_other 0.142 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_other 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_nbtor_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2769 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 9
Software Software Software Name Purpose MAR345 data collection MOSFLM data reduction SCALA data scaling X-PLOR model building REFMAC refinement CCP4 data scaling X-PLOR phasing