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Crystal structure of human CK2a with AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AT2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 25% ethylene glycol, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.93 36.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.242 α = 90 b = 78.46 β = 90 c = 82.389 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 CCD RAYONIX MX325HE 2013-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 56.82 100 11362
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 3AT2 2.5 56.82 10781 543 99.87 0.1872 0.18448 0.1835 0.23964 0.2343 RANDOM 31.914
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] -1.19 1.8 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.797 r_dihedral_angle_4_deg 23.162 r_dihedral_angle_3_deg 19.436 r_dihedral_angle_1_deg 7.198 r_scangle_it 3.784 r_scbond_it 2.281 r_angle_refined_deg 1.718 r_mcangle_it 1.618 r_mcbond_it 0.85 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.797 r_dihedral_angle_4_deg 23.162 r_dihedral_angle_3_deg 19.436 r_dihedral_angle_1_deg 7.198 r_scangle_it 3.784 r_scbond_it 2.281 r_angle_refined_deg 1.718 r_mcangle_it 1.618 r_mcbond_it 0.85 r_chiral_restr 0.121 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2817 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 57
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling