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Crystal structure of the apo-form of human CK2 alpha at pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 30% PEG 4000, 0.2M lithium sulfate, 0.1M TrisHCl, pH 8.5, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.686 α = 90 b = 46.065 β = 111.51 c = 63.675 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 315r 2008-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 59.24 99.7 0.067 0.067 17.5 3.5 29505 29505
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.8 0.397 0.397 0.467 0.245 1.5 3.6 4263
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 2PVR 1.8 59.23 29490 1498 99.6 0.1645 0.1617 0.1787 0.2163 0.2231 RANDOM 21.505
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] -0.53 0.19 0.52 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.774 r_dihedral_angle_4_deg 23.397 r_dihedral_angle_3_deg 14.662 r_dihedral_angle_1_deg 5.82 r_scangle_it 5.15 r_scbond_it 3.411 r_mcangle_it 2.05 r_angle_refined_deg 1.915 r_mcbond_it 1.25 r_chiral_restr 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.774 r_dihedral_angle_4_deg 23.397 r_dihedral_angle_3_deg 14.662 r_dihedral_angle_1_deg 5.82 r_scangle_it 5.15 r_scbond_it 3.411 r_mcangle_it 2.05 r_angle_refined_deg 1.915 r_mcbond_it 1.25 r_chiral_restr 0.149 r_bond_refined_d 0.024 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2773 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 19
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ProDC data collection PHASER phasing